If you are going to add a lift, then definitely wait to adjust any drive shafts lengths until after that is done. Just make sure you have the right yokes and flanges available for both DS's. Once the lift is in, the drive shaft place will tell you where to measure from in order for them to make shafts the right length.
How big is your lift? Back when I did a 4" lift on my 40 I had to lengthen the rear shaft. Then I discovered it put so much angle on the pinion I had to rotate the diff up and re-weld the spring pads. That caused a vibration which required adding a CV joint to the top of the driveshaft.
Randy Rosetta KDØKWX TLCA #19351 69 FJ40 "Meanie" & 1970 Boss 302 Mustang