Need Help: New Brakes, New Rotors, New Clutch

[2001GTPEWTER]

Ok heres the deal. I'm 100% done with the body of what used to be a 2001 Mustang GT. The car's body is now that of a 2003 SVT Cobra, completely repainted (again) and now I'm starting the inside. I just put in an SVT guage cluster from a wrecked Cobra (its funny to look at a car with 95,000 Miles and see 27,000 on the odometer). After I buy the leather and suede seats (3 more months of overtime) I'm done with the cosmetic aspect and will go for that Cobra Engine (minus the Eaton Supercharger) from Ford Racing. Obviously along with that comes the T-56 Transmission..Now I need a little tech help.
The rotors are rusted, I wanted to put 13" stainless steel rotors on anyway...Can I do that or should I go for the stock GT size for 2001, and can someone give me a quick 1-2 on replacing the rotors.
Next, I have new brake pads and calipers, again, I've never done brakes before...any help?...
Finally, I have an engine crane for the motor and I know how to install that, but how do I replace the clutch and install the new tranny without a lift?...Jack stands make me nervous, I don't wanna die in the garage. Also, where in this car is the starter, it seems to be in a different location than on my 1996 GT. If anyone wants a picture if what I have so far I'll be happy to post a few. I think a few good answers to THIS thread will help a lot of owners...