Most folks don't have the knowledge, or tooling to perform measurements that would be precise enough to determine which piston came from which cylinder (unless you have some major wear issues happening).
It would be nice to put them back in their original position but you probably won't be able...
Nice looking covers. You need to thing about putting in some stainless screws to finish it off.
https://www.amazon.com/Countersunk-Socket-Screws-Stainless-Thread/dp/B01HBNHJCK?th=1
I don't think its hard to keep the vmax carbs synched at all. If you don't remove the carbs from the bike, its a once a season check and typically, doesn't need much of an adjustment.
Depends on what you have done and the what wheel you use.
With a notched arm and the right wheel, you can fit a 200 tire.
My arm is extended 3" but I did not have it notched. The arm was offset a bit to better center the wheel on the bike which put the driveshaft closer to wall of the arm...
Solid motor mounts add to the problem.
A bar snake, filling the bar with sand/bb's/weight of some kind, bar end weights.
Check the motor mounting areas and make sure all the bolts are tight.
Put the oem collector on a jack or use ratchet straps to pull up close to the final height so your not trying to lift it and align it.
Loosen the header pipes up near the cylinder so you get some wiggle room.
Can't tell you why Barnett sent you extra plates.
Yes, remove the wire, half size friction and steel plate, spring, and spring seat. Install a full size friction and steel plate in their place.