I'll try to help some, but can't do it all.

Wraps do weigh something so they do slow the arrow down. Most are about 10 grains so you'll lose about 3'/sec. That's not the important part though. By adding this weight to the rear of the arrow it changes the dynamic spine slightly, making the arrow act stiffer. You may have to retune the bow slightly.

For cleaning the arrows? I just use a sharp knife or single edge razor blade held at about a 15 degree angle and carefully cut them off. The blade slides under the vane.Just don't apply too much downward pressure.Then use a quick, lightscraping action to remove any that's left and scrape off the old glue. I clean the shafts with a paper towel and 91% alcohol (drug store). Don't use isoprophyl rubbing alcohol as it has oils in it. Sometimes I use Scotchbrite to rough up the surface and clean with alcohol again.

You can also just clean the shaft with soap and water and rinse with hot water. Then let them air dry. I like the alcohol. I've used acetone years ago and it works, but don't soak carbon arrows in it as it destroys the resins that hold the carbon fibers together. It's OK on aluminum.

Probably the reason the front tip of the vane doesn't line up the same is because the "kicker" on the vane doesn't let the clamp clamp tight to the front of the vane. The only answer for that, IMO, is to change vanes.Maybe try Blazers.I never liked Quick Spins anyway as they are much heavier than most and I'm a speed freak. Personally I like the Duravane LP-400 set on a hard helical. So, no quick answer for this problem. OOPS, maybe I misread. Are you using Quickspins?

Anyway, for glue I like Fletchtite Platinum. It's slower drying than super-glues or super-glue gels but that's me. I think it holds vanes better and doesn't get brittle. It's also easier to clean off when refletching. Saunders NPV is another one I used to use. And being an old fart I am not in a hurry anyway. I've been doing this for well over 30 years.

Practice makes perfect as they say. You've got the best jig money can buy. You just need to work with it and learn what works best for you.