I found this 2012 post from another forum. It's got my head spinning...
"OK, this issue really got me thinking, so I decided to do some further investigating.
The factory parts diagrams list the Mopar part numbers for all of the parts in the transfer case, as well as the combination of engine and transmission they are used with. According to the diagrams, there were three different input gears used in the TJ. They break down as follows:
Part# 4796 956; used '97-02 with the 2.5L and AX-5 transmission, this would be the 21 spline input gear.
Part# 4796 965; used '97-02 with both the 2.5L and 4.0L and
all transmissions other than the AX-5, which means the 30rh, 32rh, AX-15, and NV3550.
Part# 4897 953AA; used in
all TJs from '03-06, with both the 2.4L and 4.0L and all transmissions: 42rle, NV1500/2550, NV3550, and NSG370
Obviously, some of this conflicts with the chart from Novak. Novak says that the 30rh, 32rh, and AX-15 use a short input gear while the NV3550 uses a long one. But according to Mopar, they all use the same one.
So I tried to figure out a way to confirm either way; I ended up looking through about a million transfer case listings on Ebay to find any that were clear on what year/transmission they came off of, and had a clear picture of the input shaft, and here is what I found:
*Note, if looking through these, disregard what the sellers have to say about compatibility, most of them have no idea what they are talking about. What I am specifically looking at is the year and transmission of the donor vehicle, and the length of the output shaft pictured.
**Also, there are dozens of cases listed on Ebay that came out from behind an AX-5 ('97-02 2.5L manual), the pictures all show a very short input shaft (which should be the 21 spline), I did not bother to link any of these since there is no contention over that one.
1999 4.0 Manual Obviously a long input shaft out from behind an AX-15
1999 4.0 Manual again And again with the long input shaft
1998, unspecified engine/transmission However, according to Novak no pre-2000 should have a long input and this one obviously does
2001 4.0 Auto From behind a 32rh, long input shaft again
2001 4.0 Auto again Another long input from behind a 32rh
2001 4.0 Auto yet again Are we starting to see a pattern yet?
2001 2.5 Auto This time a 30rh, again with the long input shaft though
Now we start to see where a shorter input shaft (other than the 21 spline) actually does start to show up:
2004 or 2005, unclear, unknown transmission But a short input shaft
2005 unknown transmission But again with the short input shaft
2005 4.0 Manual Hard to see the input shaft in the picture, because it's obviously a short one
2006 4.0 Manual And another short input shaft
So, most of these clearly contradict the chart that Novak put together. However, they all match perfectly with the Mopar part #s and application for input gears. It also fits with the transfer case I just got with a short input from behind an '06 manual. Furthermore,
I did not see a single listing that showed a case from behind a 30rh, 32rh, or AX-15 that housed a short input gear.
Here is what I think happened. All TJ transmissions except the AX-5 worked fine with the 23-spline long input gear, until 2003. Then, in '03 Jeep started using the 42rle auto transmission. For some reason, the long input gear was not compatible with the 42rle; there probably was not enough room for it in the 42rle housing. So, Jeep shortened the input gear, and for the sake of simplicity started using it also with the manual transmissions, even though they previously worked fine with the longer gear.
Also to clarify, what I am calling the "short" input gear on the '03-06 case is really within an inch of the same length as the "long" input gear. The "21-spline short" gear used with the AX-5 looks like the shortest of them all. Its possible that the shorter '03-06 gear is more what Novak calls the "medium" length. Also, it should be noted then since Jeep shortened the input gear in '03 but didn't switch from the NV3550 to the NSG370 until '05, that at the very least the NV3550 is compatible with both the "long" and "short" 23-spline gears. It is possible that the 30rh, 32rh, and AX-15 might also, but there is nothing in this data to support that. This data does indicate that the 42rle
must use the shorter '03-06 input shaft.
So, to bring this all back to the OP's issue, if you are looking for a transfer case that has a 23-spline long input shaft find
any case from '97-02, except for ones that were with an AX-5 (2.5L manual). Also, if you have a 2000-2002 with the NV3550, you
should also be fine using any '03-06 case, since apparently in '03 and '04 Jeep mated the shorter 23-spline gear with the NV3550 transmission. That should significantly increase your options for donor cases; and, the case you mentioned in the first post may be the only one you actually
can't use.
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