Manual TT's aren't that rare, but they're rare enough that I'd recommend an interested buyer to watch the market for 6-12 months and wait for the right one to pop up. When you see it, you'll know it and have to jump on it.
From a mechanical standpoint, the entire transmission and transfer case from an '05 ^ Tacoma will completely swap into an FJ with little resistance, completely with OE parts. The manual trans tunnel is still available through Toyota, as well as the clutch/brake pedal assemblies, and may be interchangeable with that same Tacoma. In all of my dealings with Toyotas over the years, I've seen one that was swapped, and it looked like a professional job and it can be done correctly. This also requires replacing and reflashing the automatic ECM with a manual ECM and disconnecting the ECT module. It would be rare to find but it is quite possible.
Having said that, you know there's some yuckle head shade tree guy who's probably done the swap, hacking things as he goes and modifying the wiring here and there. Overall condition of the vehicle should wave some red flags 1st. Where am I going with this? It might not be a bad idea to request the dealer sticker to determine whether or not the FJ you are looking at is original. That may be really hard with a truck that's 10 yrs old and the owner may not have it. Take down the VIN and call the Parts Counter representative at your local Toyota dealership and they can quickly tell you if the vehicle came with a manual or automatic transmission. Like I said above, this would be rare to find, but if you suspect foul play or see something funny around the t-case wiring, it might be worth a look.
Another red flag to look for might be the trailer wiring. This would only apply to FJs with a hitch on them. Chances are that if it has the original hitch, then the wiring is probably factory or dealer installed. If it does have an aftermarket hitch on it, I'd take a look at the wiring from the trailer plug/receptacle. See where it runs up into the left rear corner underneath. If you see a bunch of tape all around the wiring, then it may have been done by a sub-par technician. The factory wiring and module are only $100 https://www.amazon.com/dp/B009NTD3LW...vert-amazon-20
and come with all necessary hardware to wire for a trailer correctly. It's 100% plug and play. I don't necessarily think that the rest of the vehicle is bad when I see a wiring hack job, but it does indicate to me that there may be other neglect or simply an owner who isn't educated enough to have these things installed properly. Hard core Toyota folks will want it done right every...single...time, and most of the members here on the forum are of that nature. I'd even ask if he/she is a member and if so, maybe poke around their posts to see what mods have been done and how.
Thanks J.B. for posting this thread, it's about time!