Finally started the engine up after 4 months of a slow 00vi swap. Using 00 injectors, fuel rail, rear coils and valve cover, EGR uptube, 4th gen TB and iacv.
Two things going on- getting an 0606 code- misfire on cylinder 3. Also a pretty decent vacuum leak that I can't yet find; getting a constant "vaccum leak sound" and tweaking the throttle gives a big "whoosh". No stalling, though. Anyway, the rear coils and all 6 injectors are used with the 00vi I bought; all 6 injectors went to deastchworks before install (1 was slightly clogger and supposedly fixed). So, hopefully it's not any of the injectors. Swapped cylinder 3 coil for another rear coil and still got the code for cylinder 3- so its not a coil problem. Didn't have an injector issues before so hopefully thats not it. Road tested around the block and certainly didn't feel like I was running on 5 cylinders. Withough pushing it hard, the only cue that I had a misfire was hearing a slight "knocking" that came and went, was around maybe 3/4 of the time, in step with the engine speed, and could only hear it with the hood up.

Could a ground problem cause a misfire on only 1 cylinder? How about a vacuum leak?

Things I'm going to check next:
-pull plug #3 to make sure no gunk fell in to foul the connection between the plug and the coil
-find the electrical connector for the rear injectors and check resistance for injector #3
-swap plug #3 for another to make sure plug #3 isn't bad
-keep looking for the vacuum leak (read a great post on spraying some starter fluid around wuile idling and if the revs go up, the leak has been found- great idea!)
-only connection that didn't have a fresh gasket was the lower end of the egr guide tube to the egr assembly- though i dont think a leak here would cause a whoosh on tweaking the throttle
-any other ideas on things to check for misfire before I get down to pulling the upper IM?

Thanks all!

 

For anyone interested, pulling sparkplug and reseating everything did the trick for the misfire. Not sure if there was some dust/dirt between at the coil/plug contact or what.

 

Glad it worked out.

 

What are you using to control the injectors off the 00VI. They are slightly bigger than the VQ30DE injectors so if you dont have any type of afc then you are running rich.. right??