Cheap and easy first.
For the vibration, check your U-joints on the driveshaft. Replace them if there's any play at all. If your U-joints are good or you replaced them and still have a vibration, post again with what lift you have (if any) and your tire size. Also let us know if you have a transfer case drop or a Slip Yoke Eliminator.
The next thing I'd do is bleed your clutch hydraulic system. They bleed differently than brakes, so I suggest finding a post by Got it at last, IRQ or gat. Each of those members has a link in their signature to Factory Service Manuals (FSM). Click on any one of those links and then click on the FSM for your year Wrangler. Bleeding the clutch should be in the transmission section. If not, post again. If bleeding the clutch doesn't help, check out this link...Read the whole thread.
So, I thought I’d share my experience with the shifting/clutch issues I have been battling for a long time. Hopefully, this will help someone else out. Several years ago, I replaced the clutch and slave cylinder on my 88 Wrangler. Somewhere around that time, I replaced the master cylinder and...
www.wranglerforum.com
If bleeding the system and replacing the master cylinder doesn't cure your shifting problem the next thing is drop the transmission. Be sure to support the engine prior to removing the skid plate.
If your budget allows, I suggest considering changing to an external slave cylinder rather than the internal slave cylinder that I would expect your '93 currently has. There's been several reports of aftermarket internal slave cylinders failing prematurely, with some failing very soon after installation. I believe Advanced Adapters has a kit to make the changeover and possibly one or two other companies.
Emerald_YJ suggests a new clutch disc and pressure plate. That makes good sense. He also suggests possibly replacing the rear main seal while the transmission is out. That's good advice for his 2.5 four cylinder engine because his RMS is a one piece seal and requires the flywheel to be removed for access. Your 4.0 has a two piece RMS that is accessed by removing the oil pan, so it's unrelated to having the transmission out of the vehicle to change.
Several posters state that the flywheel on 4.2 and 4.0 Wranglers is either concave or convex, but not flat. This makes it impractical to have the flywheel machined if it's damaged. Most folks replace it with a good used or new flywheel if they find any damage.
Depending on your lift, tire size SYE or TC drop, you might consider replacing your input shaft bearing while the transmission is out. You actually have two issues.
1- Hard shifting into first, reverse and second gears is likely due to clutch issues
2- vibration while driving is often caused by driveline angles being beyond design limits. We need more information about how your Jeep is set up before offering more advice on that issue.
Good Luck, L.M.
