For what it's worth, I think engine swaps are a bit like surgical procedures. You want to go to the surgeon who specializes in knee replacements, rather than the generalist who does one occasionally.
You want to take your FJ40 to a shop that has done the swap you want done - many times. They’ve “been there, done that” and know the drill. They know what parts they need, and where to get them.They have the swap down to a routine procedure, which means they can do it properly and more quickly; which saves you money. But it’s also imperative that they really sweat the details so the finished product looks like the vehicle left the factory that way. That’s a level of craftsmanship that’s hard to find, and usually expensive when you do.
I think it’s also important that you establish a relationship, and open lines of communication; so they know exactly what your expectations are, and similarly, you know exactly what you’ll receive.
The reality, at least in my experience, is that things will be discovered after the project starts that neither you, nor the shop, were anticipating. That will drive the cost up as those things are addressed. So the relationship and trust both ways are important.
By way of example, and this has nothing to do with FJ40s, I’m also a sixties Corvette guy. I bought a 1966 Corvette with the big motor and it was a mess. I wanted a car I could be proud of, and I don’t have the knowledge or skill set necessary to achieve that. I had the car restored by a guy who I think does world-class work. The original cost estimate went out the window pretty early on. But the quality of the workmanship was exceptional, and he more than bent over backward on multiple occasions. Yeah, I spent significantly more than I anticipated, but I got a finished product that far exceeds my expectations. At the end of the day I got a fantastic car, and I made a friend.
I don’’t think it gets better than that….