After new wheel bearing: ABS, brake & VSC light, popping noise in tranaxle, please help (long)

I apologize in advance for the length, please be patient. I know this problem has been beaten to death but i swear I have searched and searched and the ABS, VSC & ((!)) light is always associated with people having brake work done at a non dealership. the answer I need is not in Priuschat, at least its not in the Gen II search forum and I have spent hours and hours searching so I have done my due diligence so help me out if you can:
the story:
RF wheel bearing howling at me (especially when turning left at low speeds) so I replace the wheel bearing myself with a MOOG bought at Advance Auto Parts, $101.50 + tax due to a 30% off coupon.
Howling is gone. The whole job only took a couple of hours but I must have spent 3 or 4 hours the day before here and on youtube doing my homework so no stupid mistakes should have been made. So yes I unplugged the 12V negative cable before starting, no pads were changed so the caliper slid off & on easy w/o having to compress the caliper, yes I hanged the caliper on the spring with a zip tie, yes I carefully took off the wheel speed sensor and put it back afterwards ditto for dust cover.
I rented a 3-prong puller to separate the hub assembly from the axle. I did not feel like using a slide hammer for fear of damaging delicate parts (Japanese cars are very reliable but not very tough imho) so I just took the whole knuckle/BALLjoint out (some on here report slide hammer didn't even work and dissassembly wore me out). While returning the 3-prong puller to AAP I found an empty service shop and asked how much to separate the bearing from the knuckle, $20 he asks, $15 cash i reply, deal!! Due to the aluminum knuckle i asked him to use a press instead of an air hammer, he took it over to his 20-ton floor press and a couple of loud bangs latter the bearing was out. The guy was really nice I plan to go back to him in the future as he must have spent over 10 minutes grinding and polishing the mating surfaces of the knuckle clean (while talking on the phone!!). The dust cover went on and the new bearing assembly went in easy and I used threadlocker on those bolts.
Why does everybody on here act like its so difficult to put the dust cover back and you have to spend hours lining it up correctly? It has 4 holes that the 4 hub bearing bolts go through so its basically self-aligning and idiot-proof, am I missing something here?
I mount the knuckle/BALLjoint back onto the strut, control arm and steering tie rod, everything torqued. I own but never use air tools, not even for the dreaded 30mm axle nut. I have a 2 foot breaker bar and for projects like this I have a 2 foot steel pipe I throw on the end of it for extra torque. My torque wrench only goes to 80 pounds so I'm lying when I say everything is torqued correctly. The strut bolts were as tight as my 2' breaker bar could get, and I slid the pipe over the breaker bar and got the axle nut as tight as I could. Hard work considering I never took out the dent in the axle nut and re-used it and the old dent is back in the groove so I'm confident that its not going anywhere, in all my life I've never taken a bolt or nut off with hand tools and have it be too hot to hold in my hand, this axle nut was a first for me, no need to go to the gym yesterday.
rotor goes on, brake cleaner used, caliper goes on, even more brake cleaner used, wheels on, MAF sensor removed & cleaned, throttle body butterfly plate cleaned, MAF sensor replaced, battery connected, start her up.
3 Error lights: ABS, VSC and the circle with exclamation point, my research on priuschat shows that's the brake warning light, most people also get an audible tone, I don't get that. I also do not get the red triangle of death.
So of course I know how disrespectful it is to ask questions w/o searching, so I search and learn how to jump pin 4 & 13 and press the brake 8 times, lights go away but always come back within a mile. When the lights are off that first mile is a little weird, I can feel the car jerking as if the wheel speed sensor is off and the RF corner is braking unnecessarily, its throws up the swiggle TC lines as though I'm driving on ice. So I took off both front wheels (for comparrison) and confirm that the dust cover and speed sensor are where they should be and undamaged.
As I've stated I did my homework, I know I could have done the bearing job w/o removing the knuckle and I know that by doing so I probably will need a front-end alignment, not a problem, I saved almost $300 by not going to the stealership and my car is due for an alignment anyways so no biggie.
Scarriest problem of all: when taking off from a standstill, going over bumps, and occasionally while driving I get this popping sound coming from right in front of me, I can feel it in my feet too, it almost seems like the axle joint coming out of the tranaxle is slipping and popping. To me it feels like a physical problem, not just something a toyo techniCian with his techstream software can fix.
the friendly guys at Advance auto Parts don't believe an alignment issue can cause problems with ABS, traction control and tranaxle but they hook up an OBD II reader but nothing shows up. I own 2 gen II Prii for the past decade and never felt the need to buy ScanGuage as I thought that was for engineers & hypermilers who want to know their RPMs, SOC, etc. I now find out that there is this super cheap cable on ebay called a mini PCI with the proper Toyota Software (pirated in China I'm sure), anybody try it?? Others suggest an Old POS laptop/netbook to dedicate to the mini PCI, is that true?
Any ideas as to what my actual problem is and the solution? When others have this problem most reply 'replace the ECU computer' or 'the speed sensor is damaged' or 'the ABS sensor wasn't put back'. But I took everything apart carefully and slowly and put everything back carefully and methodically. I never noticed any ABS sensor, where is that located? Can the center screw of the 3-prong hub puller push so hard on the axle as to damage the transaxle? Please help, the car will be parked until I get some good advice. I did a whole bunch of maintenance to my Prii a few years ago so I haven't been here in a while. Back then the 'experts' included Patrick Wong, John (Britprius), or Tideland (moderator). I'm not sure who is still here in 2013 and knowledgeable, I'm sure all of us here on Priuschat notice when people "move on" to a newer Prius or another vehicle and leave the gen II community hanging. Please help, thanks.

 

thanks Patrick, its nice to know you are still with the gen II community after all this time.

My friend, the backyard mechanic asked me if I lined the bearing assembly to the hub, I told him I didn't because I assumed due to all the teeth in the axle that the hub would mate up and align itself automatically, especially once I put a 150+ lbs of torque on the axle nut. He says despite the teeth on the axle hubs still have to be lined up properly during isntallation. There are several posts on PC explaining the wheel bearing replacement procedure, of course there are a few different methods depending on people's skill level and what tools you have (I don't have a super thin walled 14mm socket for example). Nowhere on any of the posts I read does it instruct you to to align the new hub to the axle, live and learn I guess.

He suspects my hub isn't seated correctly with the axle, this might explain the ABS/VSC/brake light as things aren't working the way Toyota designed them to and the computer noticed that. I think it definitly explains the popping noise in the tranaxle since the axle is a solid piece of metal vibrations would be transferred from the FR hub to the transaxle and I would have no way of knowing exactly where the popping noise originated from. I think the fact that the electric motor puts out its full torque at start and there is no loud engine when taking off is why I was able to hear the popping noise. In a conventional car the misaligned hub may have gone unnoticed and greater damage would have incurred over time.

So I re-rend the 3-prong hub puller and I'm going to try again, this time when putting the knuckle/hub back he wants me to get down and look through the hole in the hub and try align it up as best as possible, I'm going to have a helper up top inserting the knuckle to the strut while I look down the hole to line it up this time. Thanks for letting me know that the speed sensor and ABS sensor are one in the same, I'm going to clean it with a little MAF sensor cleaner before putting it back this time. I'm so angry at myself, I spent so many hours of homework before replacing the bearing that I thought it was going to go perfectly smooth, hopfully a misaligned hub is all it is, I am so looking forward to tackling that damn axle nut again.

I will let you know in a few days if all that was needed was to propery align the hub to the axle. I also had to rent strut compressors because my front struts are bottoming out shortly after having them replaced at the dealership (It was december and COLD outside!!). I'm hoping that the tech just fogot to 'prime' the strut so now I'm going to have to redo his work, hopeully the new strut just has air bubbles in it or something. He also forgot to install new rubber bellows on them and since I figure I need a front end alignment why not correct the dealers mistake first.

 

Patrick, I do have a couple of rear Monroe struts that I haven't put in yet, the instructions say to orient them in the position they will be used in and push down and up several times on the plunger to get all the excess air out. What else can explain the poor ride so soon after installation of the new struts? The Prius with less than 8000 miles on the new Monroe struts bottoms out at the end of my driveway at 5mph. My prius with 92K+ miles on original struts doesn't even bottom out at 8mph, what else could be the probem?? The front ride height of the 2 vehicles are within a 1/2" of each other so I don't think it is he springs. Every few months I check completestruts.com to see if they have started carrying "complete struts" for the Prius, no luck. If they carried the complete strut, it would make the job so much easier, faster, safer, and more complete for around the same $$$ as buying just new struts and mounts.

okay with 2 Prii and a Corolla I guess the Schley Toyota/Lexus 30mm Front Axle Nut Remover Kit is a worthwhile investment. I got a really nice set of Jesse james MAC tools & box off a desperate guy on craigslist but there wasn't a 30mm but it did have a 1_3/16" that worked great. I used the breaker bar both times applying smooth gentle power, I think that's why my threads are fine, I think if I had used an impact gun w/o removing that dent then I would get the damaged threads you are talking about. My MAC 1_3/16" socket is very nice but not impact rated but the Schley 30mm will be and with the dent remover tool the job is going to become much easier.

Per your recommendation I will get a new axle nut from Toyota, its over $15+tax from my stealership!! It took me a long time to find it online but I think it is Toyota part # 9008017238, since am waiting for the kit I mind as well buy the spindle on ebay as well, cheapest is $9.40 w/shipping, I can live with that. I have some nail punches lying around, unless you can think of a better household tool that would create a new dent better in the axle nut?

If as you suggest there is play between the hub and axle due to axle nut being loose I would expect the majority of the popping noise to be when turning the steering wheel to the left and when returning it back to the center position as it is my understanding that is when the vehicle puts the most stress on the right front hub. The fact that the noise is occuring anytime I accelerate regardless of which way the steering wheel is pointed leads me to beleve that my friend is correct and that the teeth of the hub are not seated correctly to the teeth of the axle. Perhaps you are both correct, but we will never know because I'm going to align it correctly and use a new axle nut. I'm gonna be happy if this solves everything, I don't care which one of you is correct but I greatly value your time & expertise.