1. Toss the tension gauge. I've never used one and never will. So what do you do if you get even tension and the wheels out of true or needs truing? Do you leave it out of true in lieu of perfect tension or do you true it and screw up perfect tension? You true it.

2. Sticking out a little is no problem as long as the nipples aren't binding.
3. Tools are made for sniping off the ends of long spokes. I doubt you'll find one so here are 3 tried and tue options
3a. Leave them as is and run at least 1 layer of Velox tape, 2 if needed.
3b. Take a flat bladed screwdriver and use it as a chisel to wack the extra length. Trust me....been there dont that.
3c. Buzz them off with Dremel. Never did it myself only because the boss made me do it like in 3d.
3d. File them down with a file.

My tensioning techiniue is to over dish towards the gear side then tighten the non-gear spokes to bring it back in line.