can be done, but it's much easier (and faster) with the engine out.
you need to replace the engine mount bar anyways. the tranny is much easier to work with if the engine is out.
make sure you get all brand new bushings for your new shift linkage, including the *correct* adapter bushing for the firewall. make sure the new linkage is not worn or bend before install, there should be no twisty play in the couplers.
you can do it in one saturday.
oh, btw. it's *much* easier if you have another set of hands. get a friend who knows a bit about working on cars to help you out ...
Andy