I have the EXACT same problem man...it's been bad....very annoying...somedays it's worse than others.... feels like a misfire..
But I noticed something today....
my car pulls smooth as hell when I have the silencer in. I have a greddy boost cut controller from an SW20 MR2.....and I think it's calibration might be a bit off or something...because mine stutters right around the factory boost limit. I've tried all kinds of things. Check my coils, I completely redid all the wiring by the fusebox, and got some really nice battery terminals (they were causing some of thier own problems) and it didn't help. With the silencer out, it does it, with it in, no stutter...I'm monitoring with a W/B and EGT and there's nothing out of the ordinary.
So When I get my SAFC installed this weekend, I'm going to start messing with the BCC. (I've messed with it before, but realized that was a very bad idea without some sort of fuel control...turn it one way, you get boost cut back, turn it the other way, car goes waaayyyy lean.) 
I think my BCC is the culprit and I think I can tune the problem out by adjusting the BCC and then adding fuel.
The reason I took so much space posting this is because you're using emanage and I know it has a BCC built into and it makes me wonder if the settings just need to be tampered with.
From what I've seen, most people aren't having this issue, but I've got intake, Y-pipe, no cats, RSR GTII exhaust, and a blitz LM 4" thick intercooler...and it creeps pretty good. I had to get the BCC because I couldn't even drive the car without the silencer in the exhaust because it would go straight up and hit fuel cut. Now, with no boost controller, it hovers around 15 or so PSI at all times...
so yeah...take what you want out of that post, that's just my opinion of what may be wrong with my car and your problem sounds EXACTLY like mine now...and I wanted to throw this out there because when I searched, all I found was people telling me to check for cracked coils and boost leaks...niether of which are my problem.
I will also be making a grounding kit for my car just in case....it certainly can't hurt anything!