A centered pumpkin rear axle is always preferable with the rear output location of a d20 transfer case.
An offset (to passenger side) output location is preferable with a d18 such as the Scout 80 had , whether the d27 or the "option" d44 tapered hub axle.
So...if you are having a centered d44 fabbed, then the d20 is preferred. But...the d18 will be ok though it May eat u-joints periodically. The slip joint on your existing driveshaft should provide adequate travel to move it towards the driver side and still have enough engagement...but double check that as it will depend upon how much arch ya got in the springs and the ride height with weight on the springs. It's possible that the driveshaft might need to be lengthened for optimization, but it's final length can't be accurately determined until weight is on the tires and ride height is established.
Don't mean to confuse ya! Alotta folks find and swap in a d44 out of a Scout 800 which fits perfectly on the s80, but then the driveline angle is compromised...it does work...but the offset is not conducive to optimum life expectancy of the u-joints.
Since your axles are being "built", then have the fabricator cal'c the rear pinion yoke "face" angle/spring perch mounting so it's parallel with the transfer case output shaft yoke face angle. That is what u-joints like!
Same for the front, but after the spring perches are optimized for pinion angle with the transfer case, the the axle housing "c on each side should be twisted to optimize king pin inclination and spindle assembly caster.
We shoulda had a longer talk yesterday, now that I know what ya got going on, we coulda addressed this and I would not have confused ya!