Dude, check out my mods list in my sig. With intake, plugs, headers and rockers, I'm still running a 3.4, and I think it may be a little on the small side for all that. 3.0" is WAY too wild for a stock motor, or even a mildly modded motor. Try dropping down to a 3.5" and you'll probably make more power with a stock set-up, and you won't be running the risk of splattering your motor.
Once you've done that, a 180* t-stat would be the next step, then a PCM, then you can start thinking about more ambitious moves like a cam-package or rockers.
Also curious about the Y-pipe thing, if you have a picture, I'd love to take a look.