I own and drive both, but my FJ80 still has the stock 3FE gasoline engine. They're both great trucks, but IMO they're hardly comparable - very different except for both being Toyota 4WD.
The 80 is a tank. The thing is way heavier than an FJC and everything is heavy duty. No doubt in my mind that it would take much more abuse than an FJC. The stock gasloine engine is great for trail/expedition use; it is torquey like a tractor engine, and develops good torque at low to moderate rpm's. It is pretty bullet proof too: no timing belt or chain, simple pushrod valves, 8-quart oil sump, giant radiator, easy to work on, few known issues. Mine has almost 200K on the clock and the compression is still within a few psi of new. The A-440F auto tranny is a massive beast, it holds 20 quarts of ATF, weighs a ton, but is semi-legendary for extreme performance and reliability. The 80 holds way more stuff and is much easier to sleep in than an FJC. There is lots of aftermarket stuff available. Parts still available from Toyota, but you'll usually have to order them.
Downsides to the 80: it is heavy, it doesn't start or stop very fast. It has almost 100 less horsepower than the FJC and it weighs more. It goes through front disc pads quickly. It's scary to drive in big-city rush hour traffic. Gas mileage sucks; stock it was 11-12 mpg, by adding headers and a K&N air filter and airing up the tires to 40+ psi, I've got mine up to 14-16 mpg (the only time I got 16 mpg was with a stiff tail wind in west Texas). When it's loaded down, it's hard to keep it over 65 or 70 on the highway if there are any hills at all.
Parts can be expensive, since most of them are over-engineered. No matter how well built or maintained, a 15-year-old truck is going to need more maintenance and carry more spares than a new FJC. No rear A/C.
The FJC has plenty of power, fantastic brakes, is quiet, handles like a dream, has better A/C, gets way better gas mileage. It will go as fast as you could reasonably want. It's shorter; better on the trail but worse for carrying loot and sleeping in. But it's not made with the same weight of metal or components as the 80. I guess time will tell how it will hold up to abuse.
If was going to spend any time on the road getting to the trail, or commuting, etc. I would choose the FJC hands down. But if I was going to drive the AlCan highway or the Outback, or driving in a hurricane or when The Sh!t Hits The Fan, I would want the FJ80 no question.
As to the diesel conversion, I can't say. Personally I'm not in favor of putting non-Toyota engines in one. I know a guy on the 80'sCool mailing list who is in Canada and put an H-series Toyota diesel in his 80. He's still dicking with it trying to get everything right. If/when Toyota ever offers a diesel in an FJC, I'd trade mine in on one in a second. But the 3FE gas engine is a great trail and expedition motor. If only it got better mileage.
Good luck on your decision.