well heres a couple of hints

popping out the intake manifold means super lean conditions]

either you have a big amount of unmetered air somehow getting into your
engine or....

there isnt enough fuel being added by the computer

orr.. mechanical failure - i.e. fuel injector, valve, etc

compression test the motor first - easiest
crank the fuel pressure up a few psi if u have an adjustable fpr
check your timing!!!!!!!!!!!!!!!!!!!

whats your static compression ratio on ur ls/vtec

keep in mind the gsr head increases compression compared to a b16 head.

if you say everything is good try a different computer, maybe something like a type-r basemap or something if u can