Having converted my 1974 (10/73 build date) which came with the J30 as 3 on the floor to a later H42 4 on the floor, I am much happier with the 4 speed. The gearing just seems right for the FJ40. From feel and sound you know when to up shift and the next gear is right where it should be for power and rpm.
In short, I am a big fan of the H42. It was great when I took my 40 on a 1000 mile road trip from Los Angeles to Denver.
One other thing to consider with the 3 on the tree is if the transfercase is controlled by a floor lever or the vacuum system. The vacuum shift system is fine, but needs to be checked that is is reliably functioning. I had a friend relying on engine braking coming down a hill (he lost his brakes earlier that trip, and his parking brake was busted) and the vacuum system decided to kick out of 4WD and into neutral. Ended up rolling the truck down the side of a hill. Everyone walked away (not to say there wasn't an ER visit). But something to consider. Maintenance on the lever is a bit more intuitive.
4 on the floor will have the t-case lever. But if it is a factory 4 speed, it will likely have the higher 4LO gearing.
As for value I'm guessing it will have to do with who it would be valuable to. Here on Mud an H41 4 speed with the lower first gear might be more valuable. For non-Mudders the column shift could be more valuable.