just wondering how much abuse a stock 5 speed in a 93 cherokee 2wd will take

I would guess you'll break something else before the transmission, unless you smoke the clutch out or really like banging gears. The transmission itself is pretty overrated for a stock 4.0L, and the clutch is the same size as a Mustang GT's, you should be alright.

was thinking of flipping the rear and add a locker

What does flipping the rear mean?

move the rear end on top of the leaf springs instead of under them

You could get a MJ rear some of them had spring under axles. Or even a YJ but you would be stuck with a D35. Some MJ's came from the factory with D44.

So you want to lower the rig. As long as you do enough research, and spend some time figuring out angles and whatnot you should be fine. Transmission should be unaffected, and the locker won't make much of a difference to that.

YJ rear axles had a different spring perch width, if you've gotta cut them off anyways, might as well do it to the axle you already have... Unless you get a YJ with 4.10's, then it might be worth it, it sounds like this OP wants to have some funtimes doing skids.

need to watch the pinion angle when i do it there is a flip kit for a dakota with the 8.25 rear wounder if i could use it

For what it's worth, I have abused the crap out of my ax15 + 231 combo. Smoked the clutch a few times and it still holds fine and shifts smoothly at 260k miles. Change the fluid often and it should last you a good long time.

was thinking of drag racing it it is a 2wd