Got a '99 4.0 auto 4WD 160k about 1.5 years ago. Had a warm start problem then. Initially assumed it was a fuel pump problem/check valve issue. "Poor man prime" makes no improvement at all. Quickly noticed it NEVER has a slow start issue when its stone cold. Can sit overnight or for days and crank right up on the first turn of key.
However, every single time its driven to full warm (never runs hot in Alabama heat) it will take 3-4 attempts to crank. Oftentimes will stumble for about 5-10 seconds when it does finally fire.
I hate just throwing parts at a problem but decided to do a few maintenance items that were due.
Original injectors replaced with refurbed 4 hole 784s, plugs (Champion copper), wires, Accel dist cap and rotor (brass contacts), removed and cleaned TB and IAC til it shined like new money, cleaned up battery cable and refreshed a couple underhood grounds (where are all these darn things anyway?). For the heck of it I got one of the injector insulation deals from the dealer to wrap #3 injector (heat soak?) i have searched and read on here til I am crosseyed. I've seen references to the CPS, the temp sensor, heat soak, o2 sensor, clogged cat, etc...being the cause.
BTW, its not throwing any codes.
Admittedly, I have not checked fuel pressure yet but assumed (flame expected) the perfect cold starts kinda ruled it out. I WILL check it...especially at operating temp.
Sorry for the long post but thought it might help rule out some first thoughts. Any help from the XJ addicted collective will be appreciated.

 

With the stumble after start-up,clearing after a few seconds...that could be the clearing of excess fuel from a leaking injector (which in your case, might be leaking when it's warm).
Since you are planning to do a fuel pressure check: do a leak-down test too and share what you find with those tests.

 

The symptoms kept pointing me to that conclusion too...and I was hoping the rebuilt injectors would take care of it. I guess I figured the chances of getting a leaker out of that group of rebuilts was remote. I will try to get to the FP check this weekend...this week is really slammed.

 

So the issue was there before the swap....?do a leakdown test too.

 

Thanks Roler. Yes...and problem didnt change at all after swap. I'll have to get a gauge this weekend and check it. Lots of things can happen to affect cold vs hot engine starts/running and I'll check it both ways.

 

I am going through the same exact symtoms. I had to replace a pump problem persist. Cold start fine warm start is terrible. I have good pressure no leak down. No codes. Hope someone had figured this out.

 

Search on here for "heat soak." This may or may not be your problem. It is common though.

 

Yea...i found quite a bit on the heat soak issue. There is a recall for another year (and might even be for the tJ) that involves the molded insulation piece that sits under all the injectors. I got the PN but the dealer would not sell me one because mine didnt fall under the recall.
There is also a TSB that involves the little asbestos sleeve that fits around the #3 injector for heat soak. Even though it didn't reference the '99 XJ in the TSB, I got one (cheap) and installed...and it made no difference at all.
Heat-related probs can be tricky. So many parts/sensors/hardware that occupy the engine compartment and all are subjected to cold/hot cycles and the expansion/contraction can affect tolerances.