How many splines does a stock np231 out of a 1999 TJ with a 4.0L and a manual transmission? input and output please trying to order the right parts from advanced adapters for an atlas II

The NP231 has an aluminum case and it should have a tag on the back saying New Process Gear, Model 231. New versions of the NP231 are refered to as NVG231 or NV231 which stands for New Venture Gear. The tag on the back of the transfer case will reflect the name change. Only the name is different. A NV231 HD model is used in some ZJs. Presumably this is a "heavy duty" version for Jeeps with the big V8s.

There are versions of this chain driven transfer case that take 21 and 23 spline input shafts. The 23 spline version is used behind the AX-15 and the 21 spline is used behind the AX-5 and the BA 10/5. The output for the front driveshaft is on the drivers side. Low range is 2.72 and high is 1.00.

If you own a 21 spline NP231 and you want to swap in a 23 spline transmission, you can either look for a cheap 23 spline NP231 at the junk yard or go to your local Jeep Parts Dealer and order up a new input shaft part #5300-6085. This is the part you need to convert your NP231 to 23 spline input.

http://www.off-road.com/jeep/tech/xfer/np231f.jpg http://www.off-road.com/jeep/tech/xfer/np231s.jpg http://www.off-road.com/jeep/tech/xfer/np231b.jpg

your tj should have a nv3550 tranny. it could possibly have the ax15 buy highly unlikely. if it has a rusty cast iron 1" thick piece that separates the front and back half, you have an ax15. if you dont have that cast iron piece, it is a nv3550.
nv3550= 23 spline flush mount
ax15=23 spline 1/2" stickout

the advanced adapters web site should be helpful with this
www.advanceadapters.com