it all depends on what you are planning on doing with the car, if your just gonna bang it around on the street a little then the stock T-5 swap would be good, but if your planning on really beating on it then a stock T-5 or AOD just wont cut it, to swap to the manual with a beefy tranny will probably set you back $2500, check out
www.stangparts.com , they have complete kits with tremec tranny's there, if you wanna stay with the AOD and want it strong then go with lentech street terminator for about $2000, or if your not planning on really banging on it, just get a good stall converter (PI stallion is supposed to be awesome, but pricey, about $700), lentech valve body ($350) and a hardened shaft ($250), looking at all this money for the AOD is making me think about the T-5 swap again
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88 Notch, 3.73's, Ported E7's, Explorer int. w/ ported lower, pulleys, 1.7RR's, BBK headers, off-road H-pipe, flowmasters, subframe connectors, 65mm TB, shift kit, March ram air ,MSD coil, U/L control arms, 155lph fuel pump, cheap 2800 stall, Crane Adj.FPR, best 1/4--> 13.77@101.35