hj75 rear axle in into fj45 troopie

It will but there are a few hurdles to overcome, same goes for the 5 speed.
This is from memory but it has been many years since I did the same/similar conversion and the brain is a bit foggy.
Check that the spring seats on the two housings are the same width apart, I 'think' the 45 is narrower which means you will have to relocate the spring seats on the housing.
I did a disc brake conversion to the front at the same time which required the master cylinder to be changed (used a 60 series one)
Is the 40 series actually a diesel? if so it is technically a 47 in which case the gearbox/bellhousing will bolt straight in as the engines are the same. If the 40 is actually a 45 with petrol engine then I 'think tht bellhousings are different.
You need the gearbox and transfer as a complete setup from the 75 as the transfer on a 45/47 is different and won't bolt up.
Of course once you fit the 5 speed and later transfer case you then need the 75 rear end to get a handbrake as on the 45/47 it was on the transfer and on the 75 it uses the rear brakes.
I can't remember what I did about tailshafts but think I had to get the 47 ones lengthened and shortened as the transfer ends up a bit further back.
Transmission mounts are very different on the two and required some mods from memory.
any more questions fire away as the memory might have an answer ;-))

The diff widths are thesame 75 to 45, the spring pads sound like they will need moving.
The 5 speed will be able to fit, using your bellhousing on it.
Andrew