Most 5.2L Magnums have 230HP, 300Lb/Ft torque., ZJs have 220HP, same torque, due to exhaust/air cleaner differences. They have been built since '92. The 5.9L Magnum usually has the same 230 HP, except in R/T trucks and 5.9 limited ZJs, here it has 245HP, (premium fuel with different PCM timing/fuel calibrations). Torque is around 345 Lb/Ft. The camshaft is milder in the 5.9s than the one in the 5.2L, for a broader torque curve. Mopar, Crane, and other cam grinders make hotter, smog legal, computer controlled compatable cams that wake up the Magnum engines if desired. Performance PCMs and "chips" are available from Mopar and Jet, etc.
5.2s are found in all of the Dodge trucks/vans, and Jeep ZJs, '92 and up. They are made in Detroit. 5.9s come in '93 and up Dodges and '98 only ZJ 5.9 Limiteds, and may be easier to find than a 5.2. Dodge was giving them away as a no cost option in trucks, due to a shortage of 5.2s used mainly in ZJs. Dodge builds 5.9s in Detroit and in Mexico. Manual transmissions are only found in Dodge Dakotas and Rams, not in Vans or ZJs. The Dakota and Ram 1500 PCM calibrations will work best for the CJs with manual transmissions, the Mopar reman PCM I'm using is for the '94-'95 light duty, 5-speed CA model.
The only usual problems are waterpumps, around 40K, intake manifold plenum plate gasket leaks (oil consumption,pinging-TSB updated part) around 60-70K. Some Mexico 5.9s have valve seats prone to crack, usually no noted unless overheated. Intake manifold end seals leak on the older ones, a new gasket/bolt package seems to work well. We've only seen 2 5.2s fail that weren't due to lack of oil or coolant; a loose wrist pin at 600 miles (new short block, the "old" cam and lifters are in my engine now), and a broken valve spring at 69K(no bent valve). Overall, more reliable than the 4.0L!
With the 5.2l in my CJ, it's a whole different animal, pulls hard from 2500-5200 redline in the PCM (fuel shutoff). It pulls harder than the six below 2500 also, it cruises in 5th at approx1900 RPM, but downshifting is necessary to pass quickly or climb grades. (I'm running 3.31 gears and 31-10.50 tires, .75 OD fifth). It idles smooth at 650. Averaging 14-15MPG, best of 17.2 highwy at 70, full camping load. I've put about 8K miles on it since November, no problems.
When I first put it together, I used a fan clutch of suspect origin (I work at the dealer, I get to pick through the warranty parts that Chrysler doesn't want returned), it never seemed to engage the fan. I never overheated it though it did run to the top of the green running slow through a sand wash. I bought a new HD Dodge clutch, and it's never gone over 1/3rd green. I'm using the stock 3 row high efficiency cored, late A/C type, 6 cylinder CJ radiator, stock CJ V8 fan shroud (modified to seal to the late radiator and clearanced for the new hose locations), reversed the inlet/outlet and relocated filler cap (to the middle of the top tank like the V8 CJ radiators),Dodge fan clutch with the stock CJ 19.5" reverse rotation 7 blade fan. I'm not sure on the Ford trans compatability with the Dodge, but it probably is the same. Tha Advance Adapters catalog may say if it is the same or not. Many old Mopar transmissions used the 23 spline input shaft, if I'm not mistaken. The case pattern is probably the same, the length of the input gear or the size of the pilot may be different, though, I'm not sure. The Mopar trans may have the same low gear as the Ford, too, I'm not 100% sure here, either.
Hope this answers your questions, Marty.