There is no reason to wait to get E+ if you know you want it - you can choose from seats available now, rather than what's left after everyone on the flight has already checked in.

Upgrade depends on your financial situation--business class is nice (not upgrading to first class from Y), but that's expensive. Of course, chances aren't good the upgrade will clear anyway.

As for Cuzco, it looks like pretty much everything connects through Lima, and United offers connecting service ORD-LIM, so you could do that and get some more miles on your way to status with UA (there might even be a Star Alliance carrier for LIM-CUZ).