I've had three Trackers and 2 Samurai's and all had a small leak at the reverse light switch, but nothing major. The O ring on the switch fails and it leaks. Since its a bevel fit, very little torque can be applied or the case will crack. Other than that, I've never had a major leak on any of the vehicles. I replaced the front seal on one with over 160K miles on it, but only because I was in replacing the clutch.
The transmissions are a little clunky, especially when cold. I think my current 2000 Tracker was the worst, but Redline synthetic is a real improvement; I've used it in all my vehicles. For the Trackers, I use a 50% mixture of Redline MTL and MT-90 oils in the transmission and transfer case and it really makes a difference. Its a little pricey, about $8 a quart at Summit Racing, but I feel its worth it. Do not use GL5 in a Tracker transmission, its bad on the syncros. If using conventional oil use GL4 only.
Popping out of gear could indicate a bad syncro or a loose input shaft or bearing or it could just be tight linkage.
For the $2400, the shop should have fully rebuilt the trans and used new seals and installed it correctly and made sure it worked when they were done! If it were me, I'd be stopping payment on a check until they got it right.