are you running a factory computer?
If you can manage to get a specific misfire code (p0301-4), you can swap injectors around to see if it follows...if you get a specific misfire code that remains after moving injectors, its most likely an injector seal at that location...if you're just getting a random misfire code with no specific cylinder, its most likely a vacuum leak...if you're getting a lean code, its probably a deeper issue related to the increased air flow...in which case your 440's are easily addressing that...but it could be MAF related, too...but, as always, a combination of all of the above issues could cause any number of different related codes...a vacuum leak should quickly trigger a code, also...
are you reusing injector o-rings between the different injectors? I don't have any experience with that intake manifold, but just trying to help.