We have both a 62 and an FZJ-80. The 62 is my wife's DD and the 80 is mine. The 62 is stock for now and the 80 has a few basic mods that everyone else has. Off road, the 80 stock was amazing, comfortable, and forgiving. The 62 off road is very capable, a tad more brutal, but still more comfortable than a CJ series Jeep.
If you do the basic mods, here are the comparisons....
Suspension system.
80 series, OME Medium or Heavy system will cost ~$900.00 and takes me under 2.5 hours to install including the caster bushings.
6x series, OME Dakar systems start ~ $1000.00 for the basic parts to ~$1600.00 to have all the parts to do it right. Depending on the condition of the mounts (rust) it could take me from 4 hours to a full weekend to install.
Bumpers.
There are several different styles and manufacturers for the 80 and only a few for the 6x. Cost will probably be close enough to not make much difference. A quick check on ARBs at Cruiser Outfitters shows the 6x ARB ~50 bucks less than the 80.
Performance.
The 3FE is a bulletproof engine, gear driven timing system, proven fuel injection system. The A440 tranny in the 62 has a couple issues. The output shaft tends to wear and you will hear a clunk between reverse and drive until you don't hear the clunk anymore. then it will be rebuild time or use a gear from Australia to fix the clunk. I have also seen guys just weld the gear to the shaft while it is still in clunk mode. The welding is the cheapest and easiest way to "fix" the gear issue. The other thing is they don't respond well after overheating. The tranny is only cooled through the radiator, so what many have done is to add an aftermarket cooler. You still have to keep the tranny fluid fresh on these.
The 1fz-fe has proven itself as a very reliable engine with a couple hitches. Many enthusiasts have noted head gasket issues that once replaced with the new OE Toyota gasket, have not returned. (about a 1200-2500 job depending) There is also a hose that is a real PITA to change that often gets overlooked until it blows. The A442 transmission (93-94) was used in 30,000 pound Hino busses overseas and is, in my opinion, the toughest stock production, automatic transmission in a passenger vehicle, ever. Straight cut first gears will give a bit of a whine that goes away after shifting to second. The 80 series tranny cooler is more than adequate. 93+ you will find most have ABS and therefore a Full Floater rear. Factory lockers were available and I see quite a few with them.
If I were to do it again, I would get a 93-94,(stronger tranny and no air bags), cloth interior and lockers. The leather is nice, it just doesn't belong in the bush. I couldn't pass mine up even with leather and no lockers as I have all the service history, the guy gave me a fantastic deal, and I knew the truck for a year or so before I bought it.
Hope this helps,