1991 Honda Civic Lights flicker inside while driving

I recently did an engine swap on my civic and since then my interior lights flicker while driving, however it is only when my headlights are turned on. When they are not on everything is fine. When they are on all the lights in my car flicker including the instrument cluster, the clock, and my cd player. When the engine was swapped I had switched the entire wiring harness over to the car but had to change out two of the plugs that went into the fuse panel (under the dash). I have no idea what the deal is!! Any advice would be greatly appreciated!