Ummm, interesting. So you have a 12R in an FJ40? Well, your options will depend on your budget, your fabrication skills, and how much of the drive train you want to replace (axles, TC, tranny, etc). What is behind the 12R as far as tranny and tc?
I doubt you will find many folks on this list familiar with the 12R. Is it dimensionally similar to a 22R/RE? You could make a 22RE fit, but I don't think you would be happy. Yes, more power than the 12R, but probably not enough to push an FJ40 out of the way.
V8s are common swaps into FJ40s and the adapters to make it work are available.
I've seen a modern Chevy V6 in an FJ40 and it seemed to work well.
You could install a 2F or 3FE, or 2FE.
I think we need to know how you plan on using this truck. Also, another thought. If this was a factory truck, it would appear it might have some historical value. Are you sure you want to butcher it up?