I'm using stainless bolts on my side feed injector caps, no issues at all
As for the VCT actuator which you have painted, It shouldn't really effect the performance of the car at all wether you painted it on the car or off. By the looks of it you painted it off the car, but I could be wrong. That bit there is all mechanical, the only problem you could have would be oil leaking from the front cover.
Seems odd that Something happened when you played with that cover. Maybe there is a problem with the VCT somewhere, maybe in the solenoid or wiring. Have you tried unplugging the VCT and seeing how the car runs? I get the feeling you might have already mentioned that you have done this but just in case
What ECU are you running/whens the last time it was tuned?