Your going to need to pull the transmission to drill that hole.
It kinda looks like your lower harness was never even hooked up. They did the half ass swap route. Not all of these plugs are needed. And the plug above your speed sensor should be for your speed sensor. I suggest for your own benefit you complete the wiring side of the swap. Here is a good resource.
S14 5-speed Transmission Swap - Electrical Connections
