I agree with Jeff. Getting the port work done is a no-brainer. Also, I'd get the O2 housing ported, or buy a better O2 housing (preferably with external dump to scare the Honduh kids away /ubbthreads/images/graemlins/laugh.gif ), to prevent creep, especially if you have a 3" exhaust and no cat. I can set the boost on my EVOIII 16G equipped GVR-4 as low as 13-14 psi with a 1psi or less spike and zero creep, with an off the shelf SBR manual boost controller.
Clipping, as Jeff stated, is really only necessary for the running the highest boost levels achievable by the turbo. Without clipping, the EVOIII 16G is certainly capable of maintaining 22-24 psi and producing 360-380whp. If you desire to make 400+ whp with an EVOIII 16G you'll need aggressive cams, serious tuning, and over 25psi of boost. It's been done, but it's probably easier and cheaper to buy a turbo better suited to meet those boost levels.
Clipping will definitely hurt low rpm spool. How much depends on the severity of the clip, 10-20 degrees of clip is the norm. There is simply less exhaust wheel to absorb energy from the exhaust gasses. The trade off, of course, is less rotational mass, and better high rpm performance. It just depends on your goals and particular setup.