i work on a lot of Venezualen FJ45's where this combo was put in down there. It can work fine, I hav a few recommendations from what I have seen/ had to fix:
-you'll want to re use the original bellhousing from the 45. The 3F bellhousing clocks the transmission on a 7-degree angle. You'll have to die grind some minor clearance reliefs on your 2F bellhousing for the H55f input bearing retainer.
-If you use the 60/70 transmission top cover the shifter will hit your bench seat without mods.
-Your 45 has the parking brake on the transfer case so you will want to either re use that transfer case's output shaft and parking brake parts - or convert your rear drums to the 40/60 drums with the parking brake, and you can use a 75-series parking brake cable with your current handle (this is the best way to go for sure)
-the 3F carb will use a throttle cable where as your 2F 45 uses a linkage.