Will the engine fit?

I have a 86 b2000 and I was wondering if a FE3 motor would bolt right up to the stock tranny? What would I have to change if I wanted to drop one in?

it will, you will need the flywheel/clutch with the fe3 as well, cant reuse your b2000 flywheel. there will be a bunch of wiring and parts to convert your truck to efi, not exactly for the faint of heart, but there is plenty of documentation on the swap on here and mazdatrucking.com

Yep, right here.