One time start up rattle, 4 months ago..

no, not always. it can also mean the engine wasn't fully warmed up the last time it ran, and some water was sitting in the intake manifold.
i wouldn't worry about it unless it became more consistent.
good job on the egr!

 

other than those few weak points, they are great long lasting vehicles. and when those are replaced with updated parts, they'll last practically forever.

 

There's other reasons for brief rough running of atkinson engines... Earliest sign you'll get of it being a problem is a sucking sound when you take lid off coolant reservoir on passenger side. Also, most people that have it bad have alot more than 15-20 seconds of rough running.

 

You got the EGR intake cleaned, but what about the EGR valve...the thing that clogs up?

 

Good point... We usually assume EGR cleaning is the valve, the cooler and the intake. But if you don't do all of them, you didn't do it right.

 

How 'bout intake manifold?

If not cleaned, FWIW, that's a relatively easy DIY. First link in my signature has some info, torque spec's for the manifold and throttle body in repair manual excerpts attached. No coolant lines need be disconnected from the throttle body btw, contrary to @nutzaboutbolt's video.

Check with them, might be done, but if not: just use brake clean, brushes (small diameter one for the small EGR passages (one per intake port).

Clean those ports out too, plus the injectors. Don't just wholesale spray brake cleaner in the ports. If you want to spray the injectors, stuff bits of shop towels further in first, spritz conservatively, then fish the towel bits out. Leave it clean/dry. Don't use oxy-clean or oven cleaner (caustic solutions) on the intake; there are corrosion prone inserts that'll react with it.

Used brake cleaner (you should do this over a pan) can be poured over a small tray of kitty litter (clay clump style works well) and set in a sheltered, outside loc' to evaporate. Then bag the kitty litter and dispose with garbage.