Congrats! and welcome to FJ40 club
Old thread but just want to share my 2cents
F2 is a great engine with it's pros n cons.(you might have F in it)
I'm having trouble with carb (my no.1 con)

,recently installed (with slight modification) a Toyota 3Y engine's new carb with electric choke and is now running smooth giving 7-8KM/Ltr avg.Though with 5F gears it will be around 9KM/ltr on highway.
You can install 31" AT tyres on stock suspension, just don't drive over 100 KM/hr

Installing Rancho RS55113 shocks and adding a leaf spring at back might get you fit the 33"s.
With lift kit and some modification you can put 37 and even 44 inch tyres on it though depends for which use you intend to use it mostly.
I'm not an expert in engine swapping but go for Toyota 1KD-FTV diesel if you know or have the means of figuring out it's electronics (old body new engine) ,as the stuck in snow pics show I'd go for more torque at low RPM than more HP at higher RPM.
Toyotas diesel engines like 1HZ,1HD-T ,1HD-FT ,1HD-FTE or 15B-FTE are better options in FJ40 IMHO.(not sure if these engines meet US emissions code)
In gasoline Toyota V6 5VZ ,V8 1UZ are popular swaps I have seen.
http://www.man-a-fre.com (you can find a lot of Fj40 stuff here) thhey used to make a lift kit not sure if they still do. Old man Emu also makes lift kits for FJ40.
Better to go for the essential mechanics first like front n rear disc brakes etc.
And yeah it needs a lot of body n paint job too
cheers!
MAK