I'd probably recommend not entering any FF number in (but flash your NW card for an upgrade), and then just fax the boarding stubs in.

On the E190s, do seats 2EF have a cutout for storage? Also if I am taking a flight departing 9:47 arriving 11:02 (the route is PTY-GUA), what sort of meal should I expect in business class?

There is no cutout (even for feet), but there is more legroom in 2EF than 1A (which has a cutout) , and your carry on goes up top where it belongs for all bulkhead seats. I fly the COPA E90 every month. 1A is better on your own, a nice sanctuary. I only fly SAL MGA or the reverse (25 minutes in air) so my meal is usually nuts and a rum drink or sometimes nothing.

For 2:15hrs I suspect you will get breakfast (don't forget PTY and GUA are not the same time zone)

I flew HAV-PTY-CUN 1 month ago. I have a good experience with them and very nice FA's. Im still waiting for my miles posted on AF FB....

Also, are the FC seats in the E90s the same as in the B737s?

Generally, the FC seats in the E90 are very comfortable. I flew IAD-PTY in a 737 connecting to PTY-LIM on a E90, both in FC and had a good experience in both.

Whatever you do, watch out for your EUAs..i did not get upgraded coming back at all..I knew there were open seats in both legs, but something went wrong.