It's better not to leave the motor completely stock. You should put a larger gasket on the head to lower the compression. The motor will be safe then and you can turn up the boost without worry.
You have a hard decision to make about getting a turbo though. There's a lot of different types out there and the way they make power through the RPM range. I've had 2 different ones on my busa.
Hahn Racecraft Kit - 282hp & 142 torque @ 8psi. - It makes power on a more linear curve (more rpm's - more power)
Another linear type of turbo kit offered is the Velocity Racing Kit. They make nice kits (but without an intercooler or water injection on their basic kit).
I do also own a GSXR-1000 and have a Velocity kit on it. I have it at stock compression though, which means that I can't turn it up anymore than it is now without blowing it up. I did dyno it out though at 6psi @225hp.
Did some playing around (just for kicks) and turned it up on the dyno to 9psi. The motor survived (I was lucky), but I wouldn't dare run it at that ( 262hp ).
MCxpress Kit - 316hp & 211 torque @ 11psi. - It makes power that'll punch you in the face. At 7,500 rpm's it makes max power which I stated above at 316hp. This particular system has an intercooler, which alows you to stay in the boost during top end type of runs without damage to the motor.
Without a doubt, I'd incourage anyone to get the MCxpress kit over any other (its what I have on the bike now). For what I do with a bike, it seems to be the best type for my certain applications....just having some fun kickin the hell out of people.
Dennis (themotorhead) did both my Hayabusa installs and tuning. I'd take a bike to him anyday.