Mark's of Australia makes the most painless small block Chevy conversion kit, though currently it is running around $1300 USD. It is designed to work with the 4-speed transmission, but it will work with the 3-speed if one of the mounts is altered. It has also been used with the so-called Aussie 5-speed, but I do not know if anything needs to be altered for it.
The kit inserts a second bellhousing between the SBC and the stock Toyota bellhousing. The Mark's bellhousing contains the Chevy flywheel, clutch and pressure plate. There is a long splined shaft and a throwout bearing shaft that connects it to the Toyota bellhousing. The Toyota bellhousing has the throwout parts, including the hydraulic clutch cylinder. This setup uses a Chevy starter. All that needs to be altered on the FJ40 are two scab plates that are welded to the frame for the SBC motor mounts, which are included in the kit. There is no cutting of the firewall, as the SBC is speced forward enough to clear. The stock radiator can be used. My understanding is that this kit will also work with a Chevy 292 Six, since the bellhousing pattern is the same. I don't know about the motor mounts. Advance Adaptors sells these kits. Check their website.
Block hugger header can be used, but on my setup two tubes touched the stock steering box and had to be dimpled. I'm going to replace these with cast iron Rams Horns hopefully before summer is out.
If your transmission and transfer case need to be rebuilt, this would be a good time to upgrade to a 4 or 5 speed, the latter being quite a bit more expensive, but hey, overdrive is well worth it.
Another expensive alternative is to install a Ranger overdrive between the SBC bellhousing and the Toyota transmission. This spaces the SBC forward enough so the firewall does not need to be cut.
Conversions that use a different bellhousing only often have issues with spacing the SBC ahead of the firewall. Either the firewall has to be altered, or the stock transmission must be moved forward, with all the headaches that involves.