Tranny Gremlin

Well it looks like the tranny gremlin is back on work on my jeep again. A little history first. ( I apologize if I rant a little.)
The throwout bearing went bad, so I did the works, clutch, bearing, pressure plate.
I got recommended to do the fly wheel, have it surfaced or somthing, but to save time I went and picked up a "new one", but when I got it the box said remanufactured. Needed it that day so I worked on anyways.

Get it back together to have the slave cylinder explode. (Yes it did exploded back into the clutch housing.) I figure my bad, must have gotten the push pin off or something.

Order from the dealer the new hydraulics for the clutch... they order and deliver a right hand drive kit. After looking at if for a while and the one I took out and looking at the factory service manual i see there error. So after 2 weeks of waiting on the part, Im starting over trying to get the part.
This week got the right part, installed in 20 min, all is good, get i all back together, and now, it kinda drives.

I can't shift with the engine running. At first I would stall if I clutched and came to a stop at a light. I just figured out today that I can drive in first gear with the clutch pedal pressed all the way to the floor. The only way to down shift after force shifting up the gears and never getting into 5th gear is to kill the engine put it in gear and start up again.

What is ya'lls thoughts on what the issue is. Should I reinstall the old flywheel, should I wait for the clutch to burn down, or should I just order a new flywheel.

Try bleeding the system.

The new hydraulics were pre-bleed, so there was no need to do that, nor way to do it, but thanks for the idea.

Don't keep driving it like that or you'll end up rebuilding the tranny too.

Many years between my 85 2.5 and your 99 2.5 but your description of the slave "exploding" sounds similar to what happened to mine several months ago. The 85 has an external slave and it sounds like you are describing an external one but before I continue would you confirm this and perhaps expand a bit on what happened.

IT is an external. There isn't much more to expand on the exploding, I just know that is exploded, so I replaced it. To replace it you have to get the master, slave and lines together, it is all one system. I think the issue is the fly wheel at this point. I found some note that states you cant machine the fly wheel, well i put on a remanufactured one that looked machined. I am going back in on Thursday to swap in the original fly wheel and while I am at it I'm gonna measure the difference between the two to see if there is much depth difference, we have decided the rule out the slave cylinder at the moment, and concentrate on the fly wheel.

On the slave, they may be sold as a sealed unit, but I understand you can seperate the hyd line at the master by pushing out a roll pin. I've heard mention of bleeding the system by pushing the slave cylinder in all the way and forcing any trapped air up the line and into the master reserve.

Well for time sake I ended up taking it into a clutch shop. The guy I talked to we betting money that they gave me a clutch for a camaro. Anyways, I am on leave starting Thursday and would rather have my jeep to play with than work on since I haven't had it for a month now. Thanks for the advice, I will update this when I find out what they figure the cause of the issue was.