my manual trans won’t stay in 2nd and 4th with the gasket and rubber boot in place. The truck might have a body lift. I bought it the way it sits . It has 32.5” tall tires. Anyone have a similar issue and know the fix?

 

Sounds like the body lift plus the rubber boot is causing inadequate clearance for the shifting lever in those gears, so you can't pull it into gear far enough to fully engage the detent. The body lift raises the point where the shifter comes through the floor, and it swings further at that point and needs more space.

You can check this by looking carefully at what stops the shifter from moving when you pull it into those gears.

Possible fixes: 1)You may be able to pull the shifter lever out and heat it up and bend it slightly forward. Just make sure you don't bend it too far and cause a problem in 1st, 3rd, and/or 5th.
2) Marlin Crawler and others sell short throw shifters, which will bolt on top of your tranny in place of your shifter and will likely solve your problem. Not cheap, though. The one from Marlin is $300.