I have two Foxbodies with cobra brakes and upgraded wilwood calipers for the front. the conversion is very easy, and you don't need the 31 or 33 spline axels unless you are running some searious HP for your drag racing application. one of my cars has a 347 and makes around 450 hp, on this car I have 28 spline axels and they workjust fine, on my other set up I have 31 spline axels with c-clip eliminators on a built rear end that supports my 331 turbo set up that is pusshing over 800 hp.
axel spline has nothing to do with how well the car will brake.
also I have done both getting parts from junk jard and getting a kit new from ford. if you put the kit together yourself, you will save $$$, my advise is buy new front calipers, they are cheap. I paid $235 shipped for some bullit calipers (same as cobra but with running horse) and they included the brake pads. the rear calipers are all the same for the v6, GT and cobra from 94-04. if you go with cobra rear rotors which I strongly recommend, all you have to do is trim the mounting cauge for the caliper and buy the correct brake pads (they are thiner for the cobra). asfaras the moan braket, I was able to modify a set of v6 brakets to fit the cobra set up. I cut the braket then welded it back to give it that extra 1/4 or 1/8 of an inch that it need it to clear.
v6 brake booster from a 94-95 and the master cylinder will work just fine, I also used the v6 proportion valve and my 3500 lbs GT brakes just fine. you do need the brake booster, and you will have to make it fit your Fox, you will have to slot the fox mounting holes for the brake booster and you will have to make a little room for it by beating the Lt apron, is not much room that you need but a big hammer will come handy for this. I drove the car for a while with the stock fox booster and the peddal was too hard, brakes were better than stock, but once I changed the booster they work great.
I had a 2004 cobra and I think the 90 GT stop better brakes than the cobra did. Once I added the wilwood calipers, the car stops hard.