If your thermostat isn't functioning right it can also limit the amount you will be able to drain out of the bottom drain ****.
Over heating like this seems to be the single most common complaint associated with V8 conversions into FJ40's.
Proffitt's Cruiser's probably does more of these conversions than anyone else this side of the Mississippi. Jeremiah told me they always put in a 4 core aluminum radiator with high flow electric fans as the surface area of the stock FJ40 radiator is too small. Any additional load like over sized tires, driving in the mountains, pulling a trailer, etc and you are always borderline for over heating. We have a Proffitt's built rig with this setup in a 1969 FJ40 and it has an automatic tranny to boot. My problem is getting the motor up to the 190 degree operating temp with this setup.
Do it step by step though. Get a good high flow fan and shroud first. Flow test the radiator. I know they recommend going to a high flow water pump on some of the SBC conversions. If you go to IH8MUD and read through the tech section on V8 conversions they cover all of the options in great detail.
Randy Rosetta KDØKWX TLCA #19351 69 FJ40 "Meanie" & 1970 Boss 302 Mustang