I had the same dilemma when making a ROM switch (to use either 3.0 Viper ROMs or 1.3 ROM on motherboard). What I did was run the switch wire through the centre of the monochrome video output (without modifying anything). After a while I found I never had to switch to 1.3 ROM because I can SKick into 1.3, or use WHDload for games or use WHDload kick13.slave for other 1.3 stuff.
Then I put 3.1 ROM on the motherboard and used the switch if I wanted to boot WB 3.9. I then found I didn't use the switch much because I ended up hating WB 3.9 - and WB 3.1 on 3.0 ROM worked perfectly fine (and I found a way to have HD >4Gb without 3.9).
Now I'm glad I never drilled any holes because I decided to remove the switch.
