I have a g60 ute with a 250 EFI cross flow conversion on an mk patrol 5 speed gearbox, running the original diffs with mq disk brake conversion on the front. Bear with me as ill try to put up some of what i know in some manner that i hope makes sense.
If your intending to swap out the gearbox AND the motor its best to do it all at the same time as this will save down time and costs. You will need custom tail shafts as soon as you move away from the original 3 speed, both because the drive shaft flange bolt paterns are different from the mq/mk pattern, and because the 5 speed box is longer and will require a longer front shaft and a shorter rear. This is a small job compared to what your undertaking with the motor and g box conversion.
For the mk 5 speed box to fit you will have to make custom mounts for it to fit properly, you will need to modify the transmission tunnel, and lastly you will be required to notch out the front g box cross member to give the front drive shaft the required clearance it will need for use under articulation.
the marks adaptors 5 speed gbox that was originaly made to swap in behind the original p motor wont require half as much work, it has essentially the same guts as the mk patrol 5 speed, but with a lower first gear and a higher 5th than either of the gear ratios available in the 5spd mk box.
the mk 5spd box you want is a F5W81A I believe. Which is the 5 speed box found in the later mk model patrol, 1984-1987.
this box was available attached either to the p40 4.0 petrol motor which is a more modernised version of the p motor found in the g60, or behind the sd33t 3.3 turbo diesel from the same year models. These have a longer output shaft and utilise a larger clutch and belhousing than the boxes found on either the 2.8 petrol or naturally aspirated 3.3 diesel.
Some of these 5 speeds were also found behind the naturally aspirated sd33, and the smaller l28 2.8 petrol, these have a smaller bell housing, shorter input shaft, and smaller clutch.
now the 5 speed had 3 different gear ratios available, the difference between the turbo diesel and the 4.0 being just a lower first in the diesel. The 5 speed from the naturally aspirated diesel was the lowest ratio available, and was similar in 1st gear to the highest ratio marks 5 speed available, but had a lower 5th gear.
the marks boxes had 2 ratios available to my knowledge. The higher having a 4.8:1 first, the lower being a 5.14:1. My spare marks box has the 4.8. Which was the better all around range imo. The marks boxes had a higher 5th compared to the mk boxes, again with 2 ratios availble, but both were around 0.78:1 overdrive or so. Im going off whats in my head too btw so forgive me if the exact figures are slightly off from what im posting- im only human.
Now all the bell housings and input shafts in the mq/mk family are interchangeable. I cannot see whats any different in my marks box, but im not pulling it apart just for a side by side comparo, having neither the time nor the inclination. Anyway, the theory is that as long as you have the base 5 speed then you can change over the bell housing and input shaft to whichever one you specifically need- but I can make that easy on you. The 5 speed box off the back of the sd33t mk patrol is the one you want, and its the most common incarnation of the 5 speed anyway. The 5 speed off the 4.0 petrol is whats in my patrol, and its 1st is just a touch too high, imo the sd33t one is spot on with the 250 ford motor.
the clutch for the conversion in mine is a sd33t/p40 one, with the ford flywheel drilled to suit, and I have had no drama with it to date. Its the largest size clutch made for the mk range, but is easy to beef up and the heavy duty gq/gu patrol clutch for the td42t motor has the same input shaft spline size and count, it can be used as a bolt in replacement for the std sd33t clutch, though some fly wheels may need drilling to suit- mine in my sd33t didnt........
um where was I?

nup I lost my train of thought, so thats it for now..........
cheers
kev