Farmall Cub

I am helping my Dad replace the reverse gear in his cub, we have the tractor split at the rear half about 4", have one of the shifter shafts pushed forward enough to get at the gear however we can't get it out. Not enough space between the housing and the drive shaft. My Dad is afraid to slide the drive shaft forward more. Can someone tell me where we should proceed from here.

The main shaft will have to come out

As Boss said, the main (input) shaft will need to come out.
I'm thinking that you are trying to get to the reverse idler gear, if so, it is a very tight fit to pull it out without messing with the bottom (counter) shaft. What you will have to do is after the 2/3rd shifter fork is removed and that shift rail is pushed as far back into the differential housing of the case as it'll go, and the reverse idler gear shaft is removed (bolt removed and shaft pushed forward), you'll have to gently rotate the bottom (counter) shaft with a prybar/large screwdriver to force the idler gear out the top. Installation will be the reverse. You will face interference with the case, but I have removed them before like this before without issue.

Use extreme caution as transmission cases are different thicknesses. Too much pressure rotating the bottom shaft to force the idler out and you may crack the casing. If there is too much interference, you may have to pull the bottom (counter) shaft as well.