1. Most would agree that the MGW is the best shifter around, I think you can keep the factory boot and knob arangement, but you would probably want to e-mail them and ask. Mustang Accessories
2. Personal preference really, but I like the pypes mid-muffler system.
3. No idea, Don't really care for alarms as the installers almost always do a hack job of it and screw something up.
4. Most are pretty close, but general consensus is that the JLT II or C&L racer are the best two. Tuner, just get what your local speed shop likes the best. Either the SCT X3 or the Diablo sport tuner.
Dan