I lined everything up exactly where I wanted it and tightened the u-bolts onto the new spring perches and put a few tack welds on the spring perches once I was for sure everything was in place and I had the proper pinion angle measured. 3* is about right. Then I pulled everything back out and did the welding. Almost impossible to do it with the axle installed. Besides you can clean everything like you said. BE CAREFUL to keep the frame and springs supported with a jack and stands when you cut the old u-bolts off. Easiest to cut them with an angle grinder because you should never re-use U-bolts.
Doing some marking is not going to make any difference. You line everything up with the springs themselves when the new offset front hangers and offset shackles are installed. Then you just bump it side to side, then the differential up and down to get everything in place and measured out. This is a good time to set you wheels back 1" inch if you choose to do so. May requires drilling holes in the shock mount plates.
Good luck
Have fun.