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Over the years, Jeeps have come from the factory with some great transmissions and some terrible transmissions. In some cases a different transmission can be the best upgrade to your Jeep as far as performance and reliability. What transmission you select to put in your Jeep depends on what you find and what you have. We'll assume you are keeping your engine and transfer case and that you already have a manual transmission. Also, keep in mind these are my opinions of what will be the cheapest and easiest swap for most people. I haven't done most of these swaps either, a lot of my information came from people on-line and from books (YMMV).
Generally, when swapping transmissions, it is best to match the engine with the transmission. The reason being, input shaft alignment with the clutch is crucial for clutch life and performance. Alignment can best be maintained with a OEM bell housing that has the proper input bearing retainer size and input shaft length. In other words, use a GM transmission with a GM engine and Ford transmission with a Ford engine. Since many Jeeps use the same Borg-Warner transmissions used in Ford vehicles, Ford transmissions generally work better with Jeeps. Quality after market bell housings exist to mate different engines with different transmissions, but they add to the cost and complexity of the conversion. An overview of the engines used in Jeeps will get the transmission conversion ball rolling.
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Wranglers
The Wrangler YJ built from '87-'95 and the Wrangler TJ built '97+ use a unique bell housing that is not compatible with any heavy duty granny transmission. Even the engine side of the bellhousing is unique, so there are no junk yard bell housings to keep the cost of a swap down. Since a special bell housing must be used, there is no cost advantage of choosing one transmission over another. The Jeep T-18 is not compatible with the NP-231, so Wrangler owners are best off with a T-18 (Ford version), NP435, SM465, or SM420. If a five speed is desired (and affordable), the NV4500 is the obvious choice.
'86-'80 CJs
CJs built from '80-'86 with the 304 and 258 and CJs built from '84-'86 with the 150, have a standard AMC bell housing and use the Dana 300. The Dana 300 is probably the best transfer case ever used in Jeep CJs and the transmission side of the bell housing is Ford compatible. Because of this, the best bet for these Jeeps is probably the Ford T-18 or Ford NP435. CJs built from '80-'83 with the GM 151 have some interesting options. Since the engine was manufactured by GM, it has a standard Chevy SB pattern on the engine side and basically a Ford pattern on the transmission side. The Ford T-18 or Ford NP435 can be used if the bell housing is retained, or a Chevy SM465 or SM420 can be used and a Chevy bell housing picked up at the junk yard.
'72-'79 CJs
If you have a CJ build between 1972 and 1979 with the 232, 258, and 304, you have a standard AMC bell housing and Dana 20. If you have a four speed, you have already have a T-18, but maybe not the granny version. '76-'79 CJs with a three speed used the T-150, which is bolt compatible with the Jeep T-18 and T-98. If neither is availble at a reasonable price, a Ford T-18 or NP435 can be converted. '72-'75 CJs used the T-14 and T-15 three speeds with a special bell housing. A bellhousing from a '76-'86 CJ can be used (except for the 151 bell housing).
'45-'71 CJs
The CJ-2As ('45-'49) and CJ-3As ('48-'53) came exclusively with the L-head I4 134. The CJ-3B ('53-'64) and CJ-5 ('55-'83) came standard with the F-head I4 134 until around 1971. The "Dauntless" 225 Buick V6 was optional from '66-'71. The Dana 18 transfer case was used during this time. If it can be found, the Jeep T-18 or T-98 would be the best option. Be carefull to match output spline count or get take transfer case with the trans. Folks with the 134 need to look for the fairly rare bellhousing for the T-98 or get a special bell housing. The 225 was available also with the T-98 and close ratio T-18, but this combination is extremely rare. It probably would be easier to get a standard BOP/BOC (Buick, Olds, Pontiac, Caddy) bell housing at the junk yard and convert a SM420 or SM465. One other possibility to keep in mind for people with the Dana 18 is the Warn/Saturn overdrive. This can make highway speeds possible even with 5.38:1 R&P!