to ClubCivic
An auto to manual swap requires that the reverse lights to be rewired up. For an automatic, reverse lights were activated by completing a circuit when the automatic gear selector is put into reverse. Now, you need to wire the lights right to the reverse switch, which can be found on the transmission.
Assuming you still have the automatic harness in there, you probably have a cut pigtail close to where the automatic gear selector was. You need to find the Yellow/red & Green/blk wires from that harness. Then, find your reverse sensor on the tranny....
Then just wire the wires you found off the harness to this reverse switch. No polarity on the sensor so it doesn't matter which way you wire them up. If this was your issue to begin with, your reverse lights should now work.
As for driver side only brAKE lights, are you sure it's not just a bulb issue? None of that wiring should have been modified during the auto/manual swap. Either that or bad / damaged wiring somewhere that you may need to trace down.