Dirk,
Cheaper or expensive is up to you. None of my questions were motivated by cost considerations. I don't have a list for you. But I have been for a couple of years keeping my eyes open for a nice 1st gen 4runner to swap. There is some information I have collected. But I have never tried this swap yet. So what I am about to tell you should be taken with that in mind.
I want an IFS but I also want to keep it that way for what I am looking for. From what I have read you will need a rear sump pan. The issue you will run into will be the brake booster. With a 1" body lift you sort that. With a 2" you should have no issue there. With the AC and power steering left (Me also) you will need to get a turbo truck 3 core radiator. But I would strongly recommend getting something from like "Be Cool" aluminum radiators.
Doing an auto will be cheaper. Especially if you are starting with an auto truck. The 4runner already came with a A series auto same as the Lexus. I would swap in the Lexus transmission to make hookups easier. If you plan on making this a smog legal truck you will have to go automatic. Its the only way to be legal in this state. Although there are a couple of counties up by you that are smog exempt. If you live up there then you are golden.
Jake