I'm currently building a mid-engined clubman type car using a Silvertop 4A-GE engine, box and suspension. See http://www.DIYSportsCar.com for the very beginnings of a build diary (I'm about to go into the garage and weld some more in the next 10 minutes). I'd suggest going transverse and using the Toyota box.
Pros: Easy to get, reliable, all the engineering is already done
Cons: Width and height may be problems, particularly if you want to use double wishbone rear suspension.
Attached is a photo of a complete Silvertop, box and suspension. The height to the top of the plenum is about 850mm, width from fan belts to end of gearbox is about 1000mm. Not light but that's mostly the engine. I can pick up the gearbox myself.
Hope this is helpful. Let me know if you need any more info.