I have a 3F-E in my FJ40. Yes it does come alive with a manul tranny.
There is currently a 2H Toyota diesel for sale. The 2H as I understand it bolts to the existing 2F/3F motor mounts as well as the bellhousing; eliminating that major work. IIRC it's like $1200 (not bad).
You would be suprised how well the H42 does behind the 3F-E, it's consistently ~20% below the automatic in gearing and has the same # of gears obviously. Yes, H55f would be tops, but adding more $, H42 works beautifully.
Are you doing this to your 60 or purchasing an FJ80? There are many advantages to an FJ80 over an FZJ80 (search some of my other posts & responses).
Now, regardless of 60 | 80 (and since you have a 2F block in your 60) I would consider mating the 3F-E head onto a 2F block, then you have the benefits of more displacement, lower torque curve, and fuel injection. Mated against a manual H42/H55f this combination would be fantastic; as you might know there are a few that run this combination.
Is this vehicle for long distance travel/expedition or rockcrawling/domestic use? If the former I would personally de-modernize and put in a non-US carb and manual adjust dizzy with a `professional' desmogging. That 2F with that combination would probably be able to burn any gasoline found.
People often disagree with my vehicles of choice, but if you really want a manual tranny as you stated in your linked posts, a 1991|1992 FJ80 is your best option, it'll be very $$ to get a manual in an FZJ80, whilst an H41/H42/H55f will bolt directly in (use a 2F flywheel and bellhousing) into an FJ80; there's some other complications, but minor ones like driveline adjustment. You could probably use a 60 series clutch pedal assembly and make it work quite easily in an 80.
60seriesguy made a decision to go Cummins which I respect immensely, but a 2H into an 80 would be a very SWEET stock swap. 2H lacks some power yes, but so does the 2F/3F-E in an 80 anyway.
UZJ100 "Mama Kuiser" built to look cool for the soccer mom
FZJ80 über rare "Geen", cloth'd & locked