It may be possible the thinner headgasket is at fault, but I doubt it. It will bring the head down a little bit which may throw the belt off slightly, but probably not enough to affect it this much. I'm assuming both cam gears and crank are all at TDC.

It almost sounds to me like you've got the timing off (crap idle) and there's some sort of vacuum leak (the stalling). If the EVAP isn't hooked up, is the vacuum line it's supposed be attached to plugged with something? All the other vacuum lines are hooked up and solid? I helped a guy install a JRSC on a '99 B16A2 Si a couple of years ago and the throttle body gasket was leaking like crazy and it run like crap till we replaced it.

Did the engine sit for a long time before you got it? Is it possible maybe the injectors have gummed up? Do you have someone else's fuel rail/injectors you can try? I'm running short of ideas so I'm trying to think in a different direction.