Oh by ports I meant the gamecube memory card port not the controller ports sorry if I caused any misunderstanding.I see you are trying to make a Wii laptop! Very good.
Might I suggest keeping the ports on the board intact and placing them on the side of your laptop casing to gain access to them for multiplayer capabilities? You could even cut the trace for data on the player 1 port and solder a switch to change between on-board and external controls.
In that case, I tend to just cut them out with flush cutters. My strategy is as follows:Oh by ports I meant the gamecube memory card port not the controller ports sorry if I caused any misunderstanding.