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Before you dig into into the infinite transmission conversion possibilities for your Jeep, you may what to take a look at these transmission conversion guidelines. Keep in mind, the guidelines are pretty old right now, but they still work for the most part.
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NV4500: The NV4500, aka eNVy4500, is the ultimate manual transmission for your Jeep. It is heavy duty, has a low first gear, and it has an overdrive. It is fairly common and there are adapters available for it for a wide variety of applications.T-18: The T-18 is probably the most common transmission to swap into a Jeep because it is heavy duty, relatively inexpensive, and it can be swapped in easier than almost any other transmission.
T-19: The T-19 is basically a T-18 with a synchronized first gear. Most T-19s are close ratio though, so the transmission is not as popular. Only some Scout T-19s are wide ratio.
T-98: The T-98 is the predecessor to the T-18 and it is as strong as the T-18, but it is said to have a weaker lubrication system. The T-98 was used in Jeep, Ford, and IH trucks.
NP435: The NP435 is almost as popular as the T-18 for the same reasons the T-18 is popular. The NP435 has a slightly better gear ratio range, but it hangs a bit lower than the T-18. Some say it is stronger, some say it is weaker.
SM465: The SM465 is a heavy duty, wide ratio, 4 speed transmission used in Chevy trucks. It is probably the strongest of the heavy duty four speeds and it is an excellent choice if you are converting to a Chevy engine.
SM420: The SM420 is a heavy duty, wide ratio, 4 speed transmission used in early Chevy trucks. It has a super low first that is 7.4:1. It is has a very short overall length which makes it excellent for early CJs especially with GM engines.
AX-15: The AX-15 is a good low buck upgrade for people with a Peugeot BA 10/5 or AX-5 transmission. It doesn't have granny first, but it is stouter than some other transmissions.
TF727: The Torque Flite 727 3 speed automatic is a good candidate for a low buck heavy duty automatic for CJs and carbed YJs. The TF 727 was used in full size Jeeps (SJs and J series pickups) in the 80s and early 90s. It has the standard AMC bolt pattern on the engine side and it has the circular bolt pattern and 23 spline output on the transfer case side.
AW4: The AW4 is a medium duty 4 speed automatic and it might make a good swap in in any Jeep with a manual transmission or 3 speed automatic. The length of the transmission might make it difficult to swap in some Jeeps as might the electronic controls.
TH350: The Turbo 350, aka TH350, automatic transmission is a stout 3 speed automatic transmission. It has been used in various GM cars and trucks over the years. Because it is a reliable, common, and short transmission, it is probably the best automatic transmission to swap in a short Jeep such as a flat fender or CJ-5.
TH400: The Turbo 400, aka TH400, automatic transmission is a stout 3 speed automatic transmission. It has been used in various GM cars and trucks over the years. Because it is a reliable and common it makes a good transmission to install in a Jeep.
700R4: The 700R4 automatic transmission is a stout 4 speed automatic transmission. It makes a great transmission to swap in a Jeep because it has a low first gear and an overdrive.
Powerglide: The Powerglide 2 speed automatic can make a great transmission to swap in a trail only Jeep.
Saturn Overdrive: Information on the Saturn Overdrive (originally produced by Warn) which is a bolt on 0.75:1 overdrive for Jeeps equipped with the Dana 18 transfer case.