So I got my truck back this week with the donor motor installed and there's good news and bad news.
The bad news..
The engine seemed to run fine, but started missing again after a few minutes. Uuuuuuggggghhhh! It's still missing on cyl. #4 like it was on the old motor, and I tried swapping coils, changing the plug and putting a new wire on that cyl, and I even changed out the igniter before the swap. So it must be a bad injector (even though I tested that before the swap too). The injector must just go in and out randomly (or leak) and it tested fine at that particular time. So that sucks!
The mechanic said he was sure that each injector stayed in the same position on the new motor so since it's missing on the same cylinder and everything else has been ruled out, it has to be the injector (or the very, very unlikely chance that the donor motor has a problem with the same cylinder and exhibits the identical symptoms). I think the chances of that are extremely slim, so I'm gonna swap the injector out on Monday and that should take care of the miss in the new motor.
The good...
It would seem now that the engine swap was all for nothing and it was just a stupid injector this whole time, but the rear main seal still leaked on the old engine and that would have cost almost as much as what I paid for the engine swap anyways. The good part is, besides the rear main (which is very cheap to fix now that the engine is out of the truck), there's nothing wrong with the old motor.
I just figured the rebuild shop did a crappy job and I lost faith in that motor because I had other issues like the rear main and I had to have the valves re-adjusted because they were stating to tick after a couple thousand miles. I got most of my money back from the rebuild and even though I now know there isn't anything wrong with that motor, I don't feel bad about getting the refund because I still had multiple problems and that still cost me a ton of time, headaches, and gas driving back there a bunch of times. Now that I know there's nothing wrong with the rebuild, I can sell that motor and get most of the money I spent on the swap back.
In the end, I think I'll just about break even on this whole thing. If everything would have been fine with the donor motor (no missing), I was just going to scrap the old motor assuming it had head/valve issues. But, now that I know it was just the fuel injector, the old motor isn't scrap anymore. In fact, it's freshly rebuilt with only 12K miles on it, so I have no reason to think that whoever buys it won't get 200K miles out of it with good maintenance!
So if anyone knows someone around California who needs a 3.4, let me know and I'll give them a great deal. I'll probably put it in the classifieds on here and maybe craigslist too. I think I'll ask $1000 OBO for it.
Oh, and on a side note..
My 4x4 dash light doesn't come on anymore since the engine swap. The 4wd still works (I went out and tested it last night - got it stuck in 2wd and shifted into 4hi and crawled right out), but just no dash light. I really doubt the bulb just happened to burn out during the engine swap, so I'll bet they probably just forgot to plug a wire back in. I know they'll fix it for free, but it's a long drive from my house so if anyone knows what it is, I'd like to just fix it myself if it's something easy.
All in all, I just hope I can enjoy the 4runner again and not have to deal with anymore problems for a good long time!