The 96-01 Explorer engine would be a great choice, since theyre not hard to come by and make great power. They have far better heads than the doo-doo e7te heads that came on the Mustangs, but have a slightly smaller cam. You will need to change the front cover and water pump for one with a fuel pump boss and clockwise waterpump. Dont forget to add the eccentric to the cam too if you want a mechanical fuel pump. Youll have to change the oil pan and pump pickup also. Since the Explorer switched to a coil pack ignition at some point, youll need a distributor. Ive heard people say the easiest way to go is to get one for an 85 Mustang, since that was the only year that had a carburetor and roller cam. As for exhaust, that depends what specific heads are on the engine. If it has the early gt40 heads, youll be fine with whatever you want. If it has the more common gt40"P" heads, youre exhaust choices will be considerably more restricted. You may be able to get a set of 65 Mustang hi-po manifolds which are being reproduced. Another option is to get a left side manifold from a 75 era Granada or Maverick and a right side manifold from a 69/70 Mustang. Another option, depending how good you are with fabrication, is to get a set of cheapy Hedman 88400's, and cut/weld the offending tubing. Most likely only 2 or 3 cylinders will need work. Having said all that, I would make sure the suspension and driveline have been converted to v8/5 lug stuff first. The 6 cyl stuff barely passed muster even when it was new.

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-Eric
65 Comet wagon, 60% of the time it works every time.