Will a 231 out of a TJ with an automatic work in a YJ with a manual? Both trannies are the stock ones. Does the spline count match up?

come on someone has to know

Likely, no. The input shaft will be different length and may be different spline count.
Nothing to stop you from using the front have of the YJ's 231 with the back half of the TJs ( I did this for my automatic ZJ, to gain sealed output and an RE SYE that had been on the manual tranny TJ).