What is the tranny of choice with the 12 valve swap? Might have to start looking into this and make this an out of state rig.
An NV4500 is a 5 speed and will bolt right up to it. The problem is that it won't really handle a ton of horsepower. You can get a lot of HP out of the 12 valve if you want to, it's cheap and easy power.
I have kept my 12 valve basically stock and I get 20+ mpg on every tank. My NV4500 does great and all I did was upgrade the 5th gear nut