Putting a transfer deadline on the cup though is difficult I think.- My suggestion in simplifying it so taht it can work in all nations with such different cup lengths etc. Is make it like specific to each game not each round. In order to play in a cup game a player must be with a team 14 days. So on the player page in your roster etc. it would give you like a read message 'this player has only been on your team 13 days and can not play in your cup games yet. In order to play in the cup for your team this player must be on your team for atleast 14 days'
I still think some kind of deadline would be a much better option. The problem is not the first rounds of the cup (where the teams are still building) it's the odd, sign players now and win the cup.