I am not a WJ guy, but I was pretty sure about this one, so I checked rockauto.com, and sure enough, the 231 was not offered on the 99: only the 242 and the 247. This information and my gut could be wrong, but I doubt it.
Maybe the PO of the 99 put a 231 on it? Maybe you are mistaken about it being a 231?
It looks like the 242 came with a boot on the rear output shaft. From what I can find, that is ok. The '99 242 has a 27 spline slip yoke rear output, and the '95 231 is the same.
As far as the input shaft length though, nobody can tell for sure! It is all about luck there.
'93 5.2L V8, Laredo, 242 TC swapped from a 249, 3" Coils up front and Front coils in the Rear, JKS Adjustable Track bar, K&N Cold Air Intake with Amsoil filter, Rear cargo area shelving, and KOR's Steering Gear Brace, IRO's Over-The-Knuckle Steering, Top Light Rail, Top Tire Carrier... for now...
OR If you prefer acronyms: 93 5.2 V8, 249>242, 3" FC, ~2" RC, JKS Adj. TB w/ KOR TB Bracket, K&N CIA w/ Amsoil filter, Shelves, KOR SB, IRO OTK HD steering