Gearbox choice is obviously limited by the engine you choose to fit.  For Toyota, Honda and Rover engines, generally the engine and gearbox should be pulled out of the donor car as a single unit.  This is also the case for the Ford CVH engine.  However, if using a Ford Zetec engine, this needs to be paired with a gearbox from a CVH engined vehicle (apparently the later Ford gearboxes are physically much larger and therefore more challenging to fit into a Mojo).  The Zetec bolts straight up to the CVH gearbox with no modifications, and a 220mm clutch plate should see the two mating up perfectly.

When choosing a CVH gearbox, there are a few things to consider.  An XR2 sourced gearbox has a 3.8ish (haven't found out exactly!) diff ratio, and an XR3i gearbox has a 4.27 diff ratio.  You can also use the gearbox from an Escort RS Turbo, which comes complete with limited slip diff, and a 3.8 diff ratio.

I am using a standard XR2 gearbox and I do not find the longer final drive to be a problem, especially on my road-going Mojo, but if you are planning mainly track use, the XR3 box may be preferable.