can i safely supercharge after upgrade?
 

If i upgrade my 98 GT to the Gt head of the 99+ can i still supercharge my engine (8-10 psi) safely, or will i mess up my engine?

I do believe the head swap will leave you with a higher compression ratio. I'm not sure of the exact #s, but it could be prohibitive to forced induction....

You will need to change your pistons to drop the compression ratio before supercharging after you put the heads on (putting the heads on your stock shortblock raises the compression).

Another option:
Port the stock heads and put on a roots type blower to replace the crappy intake....

will it be harder for them to install new pistons if they are already ripping it apart to put in new heads and cams?

actually if youy plan on sc your engine after pi swap it wil save time and money to do it while having the heads done it will save alot on labor and parts and the comp with the swap is 10.7:1

So what pistons should I get? What kind of price am i looking at?

Pistons will run you between 500-650.00 plus labor . peobe and modmax have excellent pistons but i plan on going with probe myself and better connecting rods.