Surging after depressing clutch

Quick background: 1996 XJ 4.0 MT 243k (90k on motor supposedly) recently purchased and finding all of the "gems". I used to own 91 4.0 AT so getting used to manual in this has been fun. That brings me to my question.

When I depress the clutch the engine seems to either stay at the approximate rpm or surge until I come to a stop, and then finally drops to idle. if I try to pull out before the rpms drop it wants to stall and then doesn't want to restart, just cranks. Also, when coasting on level ground in gear (mostly 1st & 2nd) it seems to be accelerating. So far I've taken the TB off and cleaned it well, replaced IAC with used but clean and fuel filter. the previous owner told me the plugs wires and c&r were fairly new. Pulled a few wires and plugs look ok. Any idea?

The no-start only happens when its warm and may or may not be related.

I don't know if this could do it, but have you checked the crank endplay? I'm imagining some kind of weird excessive endplay/crank position sensor interaction.

Disco the vacuum on the EGR and see if anything changes. You could have an EGR related problem. I would probably just pull it since it is so easy and then inspect for carbon buildup and actuate it using vacuum to make sure it functions correctly.