Hello hayden55,
IIRC, you have a Mazda M5OD-R1, for a 1996 truck.
Here's a good resource.
The
manual for the trans is also on that site. (PDF)
I just replaced the shifter ball supports on an M5OD-R1HD, which is nearly identical to the M5OD-R1, just has an extra bolt hole to mount to the 4.0 SOHC V6 and reportedly slightly stronger syncros and such for the higher power rating of that SOHC engine. Cover is on the top. Everything shifter-related is accessed through the top. Transmissions for the 4-cyl and 3.0 V6 are identical, and the 4.0 OHV V6 has different gearing and bolt pattern but might share parts like the main shafts and shift rails and such.
Go ahead and fix the rubber shift rail plugs, too. If you pull the top cover, you'll have it on a bench to get to easy.
If you need room to fish the cover out of the truck, remove the rear trans mount and lower the back end of the trans. That'll get it further away from the body. Be wary of mashing wires/A/C lines between the engine and the firewall, though. Engine will only tilt so far until it hits. I didn't hurt anything - I think...
Good luck!