I have a 1990 jeep wrangler, the throwout bearing in the clutch has gone out for the second time. Is there a way of using the linkage from a new model to eliminate the doughnut hydraulic throwout?

What does mash down the clutch mean??? If you get a noise whenever you depress the clutch pedal it may be that the throwout bearing is gone.

your throwout bearing is shot, and while your in there you should replace the clutch and pressure plate as the parts are relatively cheap but the process of dropping the transmission is rather involved. im not speculating it is definitely your throwout bearing

I suppose u have no clutch meaning that u did something wrong when assembling it or its not bled properly

I hope when the first clutch was replaced the throw out bearing was replaced. It sounds like you are either riding the clutch (foot resting on clutch pedal and partially depressing the clutch during normal driving) or the adjustment is incorrect. The throwout bearing should not contact the pressure plate unless the clutch pedal is depressed when adjusted correctly. The constant contact is what wears the bearing out prematurely.

A new clutch is due for this Jeep then
The throwout bearing & pressure plate as well

Check the clutch safety switch

There are 4 parts to this system. First is the clutch master cylinder, second is the slave cylinder, third is the clutch throwout bearing, and last is the clutch pressure plate. These are all the parts that can be the issue. The master cylinder is the part that pumps the fluid to the slave cylinder, which pushes on the linkage to the throwout bearing, which pushes on the fingers on the clutch pressure plate, releasing the clutch. If you drained the fluid out, first you need to make sure that all the AIR is out of the system. It's just like brakes, it will not pump if it has air in it. The hydraulic portion of the system rarely gives problems, so here's a question. How old is the clutch in your truck? If it's over 100,000 mi, then you should start suspecting the throwout bearing. Did the truck make any groaning noises when you pressed the clutch recently, and then perhaps it stopped on its own? These are signs of throwout bearings going out. Here's the bit of troubleshooting that you need. go under your truck, and find where the slave cylinder attaches and pushes on the linkage that goes into the bell housing on the transmission. Feel this linkage; it should have very limited to no movement. if it moves significantly, then your throwout bearing went out, and you will need to replace your clutch and throwout bearing. If not, then it's the hydraulic portion of the brakes, and you'll have to troubleshoot between air in the system, master cylinder failure, or slave cylinder failure.

Try adjusting your clutch as it is clearly not disengaging properly in second, you might also try adjusting your shift linkage.

If you have had the flywheel cut, have a clutch with a different release height (different finger or diaphram design & height) or a remanufactured pressure plate, or all of the above, you may run into this problem.
Small differences there translate to a large difference at the pedal. On linkage type designs, there were several options including longer/shorter throwout bearing or adjustable fork pivot ball. Hydraulic systems should compensate somewhat, but if you are beyond the travel of the slave cyl, I'm not sure there is anything you can do from the outside. I would check that there are no air leaks. If you have an external slave cylinder you may be able to make a slightly longer rod that connects the slave to the clutch fork. I really can't think of anything else to do at this point.
Hope this helps a bit.

Assuming what you have outlined has been done correctly, several possibilities exist: 1. You have the wrong throwout bearing installed
2. You had the flywheel resurfaced and it is now beyond the travel limit of a hydraulic actuator arrangement. 3. You have an entirely different pressure plate finger height, or a resurfaced "rebuilt" pressure plate which is again beyond specs. (or any combination of the above)
Your problem is likely to stem from this. You changed the Pilot bearing in the end of the crankshaft, correct?
Aside from taking the entire thing apart again, the only thing I can recommend is to make sure that the clutch pedal linkage and bushings are in good condition. Anything that limits clutch pedal travel should be repaired. If you have an external slave cylinder, you might want to make a new actuator rod, a bit longer than the stock one.(it would be between slave and fork if you have one at all) If you have a hydraulic throwout bearing, there is not much you can do to help without tearing it apart!
"Though hydraulic systems are great space savers, the older fully mechanical clutch arrangements gave you far more adjustment options with which to overcome problems such as you now have.
Good luck!