A minimal rust factory diesel 40 series are very hard to find, and/or very pricey.
If you can do all the mechanical work, then 100% yes go for the best body you can find...and if you aren't afraid that might be a non-runner no engine. Which could be OK if you want to swap to diesel.
LHD diesel will mainly be Canada...big rust issues, but there are other places to look.
Are you set on diesel?
Would you consider a swap?
There aren't many (no factory I"m aware of) 5 Spd US Market FJ40's
Toyota Diesels are great, but they can be pricey. Ask me...I just rebuilt my 13BT, new turbo, rebuild Injection pump, injectors everything. Injection Pump and Injectors alone you are looking $1,500+ on the low side. The non-turbo 4 cylinder Toyota diesels are quite slow and usually by this age are in need of some maintenance.
This all depends on what exactly you HAVE to have. diesel? 5 Spd?
Me, I would start with the cleanest, least rust FJ40 body I could find. Then at that point decide if I"m going 2F, hi-po 2f fuel injection, diesel swap, V8 swap whatever. The h55F 5 Spd is a great transmission from Toyota.