On my Car I ignored the first rule of Car Building-keep it simple stupid (KISS)! I have a lot of electronics (Power Door locks, Power Windows, remote Door Locks, EFI, redundant Sensors (Fuel press., Oil (2), Coolant (2), Trans Temp, etc.), GPS Speedo, more-

I had (have) the same problem you are experiencing, and I chose to route my Wires through the toe board as well-with all of my EFI harnesses and such, I couldn't put them through a port (waaay too many), so I took some Belting and aluminum sheet and made a "port" to fit the toeboard outline and used the belting to seal the Harnesses (hope that makes sense) and, I used nutserts to hold it down-

It completely seals my Floor (and, being the Aluminum is polished,
it looks reasonably well)-hope this helps (if you have a lot of Wiring like me)-