All DONE!!! Thanks HeliMech and others for their advice, and support.
1. Make sure you buy the right parts
I got copper crush gaskets for a CBR900rr. The guy thought I was looking for those and I didn't bother checking. Oh well, they took care of me and exchanged them for the ones I needed.
2. If going the bolt on route, a muffler gasket is required.
3. Taking out the Y-Pipe is easy with a cutting wheel on a dremel. If not saving it, it's a good option. No need to remove the shock or jack up motor. Just a rear wheel stand.
4. PB Blaster on the studs/bolts. When you think it's enough, add more.
5. The new header is easier to bolt up with the radiator removed. A second set of hands helps a little too, but, not necessary.
6. You can use the plate that holds the outside of the luggage bracket as a mounting point. Just remove the rear screw, loosed the front, and mount her up!
7. 96-99 GSXR750 cans bolt right up.
I took it for a spin to see how it runs and its really nice. The combo of flapper mod, the 20000 pound weight loss of losing stock cans, and the lower center of gravity make it run MUCH smoother and handle way better. Its peppier, yet smoother. More responsive. I will post a pics and video of her running tomorrow.