I've done exactly what you want to do. '79 HP D44, both tubes cut and shortened, but I went a little off track when I had the diff moved as far as it would go to the left. It gave more clearance from the oil pan and made the front driveshaft run a little straighter. I paid $195 to have the work done back in '02.
If you have factory shafts cut and resplined, it won't be the splines that fail first so don't even worry about it. You're using a 30+ year old part that doesn't have the metalurgy of aftermarket shafts. I run full circle clips and 760X joints and have broken about 4 shafts (all long side). It looks like all occurred due to the ears on the stub shaft or the axle spreading. I'm finally out of spare shafts, so the next set I get are going to be custom NEW shafts. But, if you're not going to wheel too hard and/or run 38's and a locker, resplines will hold up just fine.
As far as the rear goes....no clue here.
One thing a lot guys who don't live in the Northeast don't realize is that full width axles are very limiting on a lot of trails. If you want to just play on the rocks they're fine, but get on a tight trail that was created 50yrs ago by MB Heeps and you ain't going there. I've had problems with stock width axles and 16" wide swampers.
Greg