So the proper way to calculate port length with two ports is to plug the numbers in for one port and divide your box volume in half. So for a 3.2 cu ft net volume box with two 2" x 15" ports you would calculated it like a 1.6 cu ft box with a single 2" x 15" port. In your case, if you are tight on space my suggestion would be to use one port if you can. It takes up less space due to having less internal panels. Also 60 sq in of port area is a bit more than you need. There is nothing wrong with having more than you need and with multiple ports its better to be on the high side for port area since multiples port are less efficient, but if you switched to a single port, 45 sq in (3" x 15") would work just fine.
With regards to the SA-15 vs E-15, I didn't see that you were looking at TWO E-15s vs ONE SA-15. Either of those would work well in terms of power handling, but the two E-15s would have needed a box twice as big.