I did this swap. I don't know exactly what went wrong during mine, but it was not a direct swap. From what I understand the bellhousings may be a different size. Check that before you swap them because if they are I think you can just take the bellhousing from the AX15 and put it onto the NV3550. I did not do this, and once the NV3550 was installed the rear driveshaft would not go back in. It was a few inches too short. I ended up doing an SYE with a different shaft. If you already have an SYE then you should be fine to throw the NV3550 in as is. 
I paid $650 for mine with 58,000 miles on it as well as the NP231 still attached to it. It came complete with the shifter and clutch and everything.
when i did my motor swap in my yj using a tj motor and rubi case the nv 3550 that i received had a bad first gear due to the accident, i looked and looked, but could never find anything around here, i ended up driving up past Scranton Pa and and picking up two nv 3550-s one from a jeep and one from a truck or somthing. i think i paid 350 for both, we tore em arpart and they were in awsome shape, so i used the orginal for parts, put one in my yj and sold the other for 700- the moral of the story is dont be afraid to drive and look for a deal.
OK still trying to decide which route I want to take with the replacement of my trans. From what I have heard the NV3550 is a direct replacement of my AX15. So what im looking for is, someone that may have a connection with a Scrapyard that might be able to source me a good deal on one. From what I have seen the going rate is $650-$750 in this area. Anyone with info on a trans or info on the swap please speek up, Thanks in advance,
Andy
Here's a write up.
This guy has a YJ but used a bell housing from a 98TJ.
Sounds like it was pretty much bolt in.
Unless someone just doesn't know what they have you probably aren't going to find one for cheap.
The NV3550 is a very desirable tranny so holds a good price.
It's actually much stronger than the 6 speed that replaced it.
Andy here's one on ebay in PA. http://cgi.ebay.com/ebaymotors…uckQ5fPartsQ5fAccessories
I'm 99.99% sure the bellhousings are interchangable between a AX-15 and the NV-3550 as far as a AX-15 goes lets just say I'm on my second one now my Jeep has over 215K on it but I'll never spend money on a AX-15 again.
I'm thinking yes as well.
I'm not sure what he's including for the $450, but the bellhousing you can just use from the AX15 if that's not included. Some people also don't include shifters, but you can install a short throw in its place. That's assuming it's just the transmission and not the entire assembly. Either way it's a good deal.
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I believe he said it comes with everything, but either way I should have most of what I need.
I am also looking at clutch kits, Anyone have anything bad to say about this one. I know you get what ya pay for.
http://www.rockauto.com/catalog/moreinfo.php?pk=1381784
Andy
I wouldn't buy the very cheapest one you can find, or you will be replacing it again before long.
And driving off road and in the sand is pretty hard on clutches.
The LUK is supposed to be good and same as the OE.
PM surfrider, he's been through a couple. Can't remember what he used, maybe from NAPA.
I realize you were probably referring to the clutch brand but Rockauto has some very good parts for some great prices. I have spent waaay more with them than I planned for but everything like service, shipping, and quality was top notch. 
Why not go with that ACDelco kit for $141?
Andy its gone a cost about 400 but I would go with the centerforce 2 clutch or even the the original centerforce. It may be the last clutch you buy. I bought mine about 8 yrs ok and have not had to replace it yet. I just put a new throw out bearing in and the clutch has about 50% left on it. For what its worth I grenaded my transmission with this clutch by pulling trees / logs and being stupid. 
I have the centerforce stage two in mine with their cluth plate and flywheel, it's really a sticky clutch but overall not to bad.
Cj-
FWIW I have never seen ANY positive feedback regarding the Centerforce clutches in a Jeep. Mainly because, as said below, it is "sticky" and somewhat hard to engage. The 4.0 simply doesn't have enough power to ever need it. I purposely slip mine all the time and it is still in great shape after 55,000 miles...
If you buy from rockauto make sure you use a coupon, there's almost always 5% coupons available if you take a couple minutes to google for one.
FWIW I have never seen ANY positive feedback regarding the Centerforce clutches in a Jeep. Mainly because, as said below, it is "sticky" and somewhat hard to engage. The 4.0 simply doesn't have enough power to ever need it. I purposely slip mine all the time and it is still in great shape after 55,000 miles...
X2
"Sticky" clutches are great for the track or mud bogs but you will be better off with something more mild-mannered around town or off road.
I realize you were probably referring to the clutch brand but Rockauto has some very good parts for some great prices. I have spent waaay more with them than I planned for but everything like service, shipping, and quality was top notch.
Why not go with that ACDelco kit for $141?
I meant the clutch brand.
I've heard lots of good stuff about Rockauto.
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