I don't care for half doors either. For me it's either full doors or just take them off.
The options you have available are plentiful. You could: 1) sell the 4:10 axle set to someone wanting to run 31" tires, and regear the other set to whatever tire size you settle upon, or 2) run 31" or 32x11.50-15 with your 4:10 axle set and sell the other set of axles for profit.
I would love to find a set of 4:10 axles close to me, as I just acquired a brand new set of 31" tires on Jeep rims cheap.
Whatever tire size you do choose, be sure to use only load range C tires on your Jeep, for ride quality. If those 35's are load range E, sell them.
Pay close attention to all of the rubber bushing in the 2 Jeeps, I would tear them both down, inspect everything, and reinstall all of the best parts onto the good frame. Then part the rest out and sell for funding or more new goodies.
Be sure to open up the pumpkins of all 4 axles, you want to look for aftermarket lockers or limited slips, and keep them for your Jeep. Get a paint marker, and mark your input shaft, and axle, count your turns of the input to 1 turn of the axle, that is the actual gear ratio. I say this because the axles may have been regeared, you may not realize what is actually in there.
Consider installing a Aussielocker in your front Dana 30, I just ordered one for $246 shipped(and I don't even have my Jeep home yet.)
If you have Dana 35 rear axles, look for aftermarket 30 spline axles in them, and do a super 35 conversion kit when you go back together with your Jeep.