it will fit. you will need to swap out the fuel rails for the return style system (not sure if the n/a rails are interchangeable with the s/c ones), but for the most part it will fit. you will need to route the belt the same way the 99-01 saleens have it routed (ford changed the routing/added an idler in 2002), and i think that should be it. the strut bar (if you have one) wont fit anymore, prob have to get one for the s/c saleen. everything else is a simple bolt on. prob gonna have to get the throttle and cruise control cables for a saleen.
for the intake/coolant ports, dont worry about it. its the same as bolting on the PI intake to NPI heads. the coolant ports ARE sealed with just the PI gaskets, but you use RTV just as an insurance policy. the supercharger will bolt on perfectly, the saleen's use the same heads as the GT, so no need to worry about it not bolting on or anything like that. not sure what you are going to have to do with the return tube under the manifold/supercharger tho.