Unless you can find a used one, just getting it rebuilt is the "cheapest" option.
When I got mine done, I also got a slightly higher stall put in it (2500 I believe. Isn't stock 2200?) a shift kit, new cooler lines and the rebuild.
Cost a little over $1300 all said and done.
98' Mustang GT coupe, CAI, trickflow 75mm intake, 3.73 gears, O/R x-pipe, flowmasters, short throw shifter, 24lb injectors. 183k miles
95' Mustang GT vert: AODE, 2.73 gears, O/R xpipe flowtech mufflers , 410,000~ miles. (totaled, sitting in yard)