Not exactly. I'm not sure if you can use the 99+ spindles. If they are the same as the 96-98 then you can yes. 94/95 spindles don't put the wheels out as far as the 96-98 spindles do. I personally prefer the wider stance of the 96 spindle, I have had no clearance problems with a 255 wide tire. Others have clearance problems with the spindles. The choice is yours. You will need to get washers to put under the crown nut on the balljoint in order to use a codder pin. Or get the shorter 94 balljoints. Once you do the spindle swap you will see that the struts don't really fit correctly, there is about a quarter inch of slop in each direction. I recommend pushing the bottom of the struts as far forward as possible and using washers behind them to take up the room. This will increase your caster which our cars defanently need more of anyway. After that, the rotors and calipers with brackets will bolt up. One of the brake hoses will bolt up. The other will not because the fitting on the hose is too large. Get the proper adaptor to make your life easier, or cut the smaller fitting off the solid line, put on a bigger one, and re-flare the line. Now that it's all installed and together step back and admire your haenous toe-in. Get under there and turn the tie rod ends out alot. You can get the wheels straight enough to get her to an alignment shop using a tape measure to measure the distance between the two front edges of the wheels vs. the difference between the two rear edges.
Now to the back, the 94-98 axles are the way to go. If you want them 31 spline, you will need to go aftermarket I believe. The 99+ axles work (I did it for long enough to drive it to the shop and say "You gave me the wrong axles!") however they're very long and I don't know how much of the axle is actually on the bearing. Furthermore with axles that long your wheels will hit your quarterpanels when the suspension compresses, aswell as the calipers have to be spaced out from the backing plates to line up with the rotors. You will want backing plates aswell as the brakes from any 94+ mustang. The rear is very straight forward. Pull the old axles out and all the old brakes aswell as backing plates off. Re-assmeble with the new hardware, fiddle with the brake lines a bit. If you use v6 or GT rear brakes, grab some pliers and pull the springs off the stock parking brake cables. Follow the cables to the floorpans and find the bracket that secures them to the floorpans and remove it. This will allow the slack needed for the cables to reach the new rear calipers. Attatch the cables to the calipers and then find a new home for the brackets. Call it Miller Time and admire.
Lastly your stock master cylinder and proportioning valve are all wrong for these brakes. There are alot of options on master cylinders. For simplicity the 99 GT master and prop valve is a solid choice. Also, on the passenger side under the hood near the hood hinge, you will see a coupling in the solid brake line. This coupling is actually a check valve which keeps pressure in the rear lines even when your foot is off the brakes. Necessary for drums, not good for discs. So pull that thing out and get a 3/16" union to replace it with. Or alternatively you can put an adjustable proportioning valve in there so you can dial in your front to rear brake bias.
If you get cobra rear brakes you cannot use the stock parking brake cables, get ones for the 94-98 mustangs.