For starters and without in depth analysis, I would recommend coach on the eastern leg (1 night) and sleeper on the western leg (2 nights).

I have done this and it is a "natural" break, rather than trying to break up the 2-night segment. The eastern sleeper was also more expensive per night than the western, so it was a better deal.

I would not expect Amtrak crews on board to accept any voucher. They would likely say "what's this."

Upgrading on board is hit and miss. You are not in the busiest season yet so it might work.