Excellent work...
As far as the turbo...this is my nerdy hypothesis...although what Dana said is most likely the correct one...
Its been a while since i have seen the stock T-25's compressor graph...but I vaguely remember it being near 275whp or so before it started to take a dump on efficiency...Turbo's push air...not boost...boost is just a vague term explaining the air pressure "increase" over ambient...but any turbo basically has a hp threshold in which it can only push enough air for X hp...this could get way to mathy, so I will save all that...but you need X amount of oxygen mixed with Y amount of gas to make Z hp...Different turbo's push different amounts of air, despite raising the intake trac's pressure the same psi...meaning a t-25 at 10psi is not pushing the same amount of air as a bigger turbo at 10psi...
So thats where this is going...I would be willing to be that you are right on the effiency limit for the stock turbo...which is somewhere between 250 and 300whp I think...with freeing up the head and intake manifold like that, you are allowing more air to enter the engine at a given boost level...but that doesn't matter if the turbo is pushing its maximum amount of air that it possibly can...The engine is ingesting more air faster than it could before...and the turbo is supplying the same amount of whp basically, just at a lower pressure above ambient...the lack of restrictions is allowing it to flow air easier than it did before though...
So it could simply be that the compressor wheel just can't spin faster, because of its limited size and restrictions to the turbo itself, to create more boost...but its flowing probably the same amount of air it did before...just at a lower boost level...Your 1/4 times lilustrate this...you were close to what you were before, albeit with 3-4 or so less lbs of boost...illustrating that you are making about the same whp you did before the intake mods, but at a lower boost level...further illustrating that time is up for the turbo...you have reached the whp limit for that thing...I am such a dork...