Rust on coils

I recently started getting a really bad misfire situation on my 2012 prius. 3 of the 4 cylinders threw a misfire code plus a random misfire code. the cel came on while driving in the rain and the shuddering started soon after that. Mostly during light acceleration. Seems to smooth out during harder acceleration and at faster speeds.
Pulled the coils today and all 4 of them looked like water had gotten in. Heavy corrosion and powdery rust.
So I'm thinking this is my problem. Is water lethal to a prius coil? How do I prevent water from getting in again? I have taken the wiper cowl off several times in the cars life so I'm geussing that's were it's getting in. Is there any way to seal the coils better? BTW the car has about 250000 miles and the engine(and coils) about 80000 miles.also it has been weeks since the rain and the coils were dry. With the car intermittently running bad and getting poor mileage.

 

Yes other than a couple minor issues I have yet to resolve all went well with the swap. If you remember I ripped the steering column in half because I tried to seperate it in the wrong spot. It bound up and pulled apart at the telescoping joint. Well I ordered a used one on eBay and that thing rattles to hell. It is very irritating. After a bit of research I found that this is a known issue with the steering columns and I feel that the ebay seller stuck me good. I've thought about installing a grease zerk and pumping it full of heavy grease but not sure if that's an option or not. The other issue is the sway bar bushings(I believe). I replaced the struts along with the engine hoping that would fix the clunking noise but it didn't and I haven't had a chance to order the bushings yet. I need to get that done. But first I need to fix this misfire problem. Can a coil go bad to where it performs ok sometimes and not OK at other times? Or do they just go completely dead?

 

Replacement engine had around 70000 miles on it when I got it. We have put 15-20000 miles on the replacement engine. I never even checked the plugs or couls when I did the swap. Yesterday I pulled the coils,plugs and intake manifold to check the egr passages.i used the same Intake manifold from the engine I pulled out. The one on the replacement engine had a hole in it. I had previously cleaned the egr passages on the manifold about 10000 miles before the engine went kaput. So it was clean.. Egr tube was also good. No idea what the egr valve or cooler looks like. I ASSumed they are OK as they have less than 100000 miles. I do hear some noise that I suspect is coming from the egr valve while the car is running. Holding a screwdriver to my ear and on the valve reinforces my suspicions.
I am going to have to revisit the coils as I didn't closely examine them. I do know that all 4 of them were pretty rusty.
I've owned the car since New and it has never been power washed. I did spray the engine bay down while I had the engine out. Avoiding electronics.

 

Forgot to say the plugs that were in there looked like the originals and they were pretty rusty as well. So I pulled the ones from my old engine and cleaned them up and put those in. They only had a few thousand miles on them.it didn't help any

 

Cleaned throttle body and maf sensor. My next step will be to swap the old coils and see what happens. Those were left out so those are a little rusty as well but they haven't had direct contact with water.. The injectors looked clean when I installed them but I know that means nothing.

 

Well I replaced my coils with the old coils and nothing changed. There were no cracks or burnt marks on the boots. Only the rust. Tried unplugging each one while the car was running to see if any 1 didn't make a difference when pulled but as each one was pulled the condition got worse.(not sure if that was a good idea or not). Pictured are the coils and spark plug that was in the replacement engine. All of which has been swapped out from the older engine. Using my Bluetooth scan tool misfire counter I picked up misfires on all 4 cylinders. But they seemed to show up while the engine was running fine and not during the death rattle. I don't know if it is counting in real time or not though.

 

Here is the pics. Couldn't get them through on last post.

 

Yes they are rusty. Mostly around the top portion but as you can see the plugs are rusty as well.
Is the video freezing?

 

Yes it only seems to misfire during idle and very light load/acceleration. Also getting horrible mileage. Ranging from 27 to 35 mpg depending on the duration/driving conditions of my trip. Up until I started getting this issue I was consistently getting 45 - 47mpg.im not sure if I know how to read the trim levels. Might need to purchase an additional pid pack. I can see the demanded a/f ratio and the actual a/f ratio(is this the same as trim levels?) which is pretty much the same.. iirc it's around 14.5.i could be wrong on that number.

 

Do other brand and model cars with this same 1.8l engine experience these same symptoms or are they exclusively prius problems? Perhaps I could do some research on those forums as well.