That'll be ok... do yourself a favor and spread the lower torque boxes like
@RacEoHolic330 did with all thread, washers, and nuts before you try to fit the subframe in the front. It was a massive PITA for me and my Dad to do it, it took us 2-3 hours to force it in there with jacks since I didn't spread them first. As for the removal tool, use plenty of anti-seize and DO NOT use power tools as per MM's instructions. In fact, I found it's much easier to take a drill and a small drill bit and make lots of little holes in the rubber bushings before you try to push it out as that will help immensely!
Also, while you're at it, for not much more money, go buy these and install them too! You will regret leaving the factory rubber in the upper/
lower control arms and Diff if you don't replace it while it's out...
Prothane Mustang Irs Control Arm Bushing Set (99-04) Cobra 6311BL
Maximum Motorsports Mustang Rear IRS Urethane Differential Mounts w/ Tool (99-04) MMIRSB45