1) that does sound steep for gears and install, but if it includes the axle swaps then I think it’s fair
2), 3), and 4) Why only front and rear UPPER control arms? You definitely need rear lower control arms too in my opinion.
6) no idea how long the compressor will take.
7) assuming they adjust the arms during control arm install, the alignment is an easy job that could cost you nothing. The only thing adjustable is the toe.
https://wranglertjforum.com/threads/how-to-align-your-jeep-wrangler-tj.85/