And im worried that the ping will do a too big difference so this will just be: Na wins on na, eu wins on eu.
Do three rounds on the NA server, then switch to EU and do three rounds. If either teams gets a majority of the victories they win. Casualties should be counted after every round so that if both teams win their three rounds the team that suffered the least casualties in total wins.
That should be a fair solution and not at all hard to carry out.
For the selection of the players, it won't be the absolute top 60, cause you will never get them all together at the same time. Just pick a date, let people sign up. Put a council together for each team that picks the best out of the sign ups. Join ts, play and let EU celebrate their victory. It's really not all that hard.
My only concern is the timezone difference, one team is going to get majorly fucked over because they have less players available due to shitty time. Thats why I suggest putting the battle on the NA server on EU primetime, and putting the EU battle on NA primetime. So that the better selection of players goes to the team with shitty ping. Alternatively you could also find a time thats equally shit for both teams and do the matches back to back.