A good stock Fox booster (key being a good working unit! ) and your stock MC can work very well with the setup you have. You will HAVE to disable the OEM proportioning valve and install an aftermarket adjustable unit for the rear discs, but other than that it should work fine. The OEM M/C is 21mm or @ 7/8" so the pedal travel is good with a good feel once everything is bleed and adjusted properly. The 94/95 Cobra 15/16" MC will feel very similar and the 93 Cobra MC 1" bore will give you a bit harder pedal with less travel in most cases.
No center cap issues with the SN95 front hubs and spindles. That issue has to do with the OEM spindles/rotor setup or similar swaps such as the Lincoln, Ranger, SVO.
The 03 Bullitt wheels should be 17X8 with a 30mm offset IIRC, and they will fit pretty well in the rear with the 94-98 rear axle assembly. You will still want to roll the rear fender lips for clearance to be sure, especially depending on tire size. Good Luck!
I personally am not a fan of camber bolts, your opinion may vary. I personally install Maximum Motorsports CC Plates on all my Foxes and I have no issues with getting them aligned and ALL my Foxes run SN95 spindles and brakes.