I would like to know which 5 or 6 speed manual transmissions are compatible for an 1988 corolla wagon all-trac since its 4wd what can I use it is automatic currently and and going to convert it to stick. Any help appreciated.

If you are keeping the 4afe stock engine, then your only option is a 5spd manual from another all-trac wagon. Trans code is E57F5. I am working a a hybrid using parts from a newer narrow E series trans. More on this over at alltracwagon.net