With the lights you could always just re-wire them to whatever switches and relays you need them to be yourself (using the FSM previously posted). Sometimes its better to just not even try to understand wtf the other guy was thinking
For the idle, I wouldn't think the plenum would matter, but if you can easily convert it back just to rule it out, it's probably worth doing.
If you can't find any vacuum leaks, I'd say try inducing one. Pull a vacuum line going to the fuel pressure regulator or something. It could be that the engine is just starving for air, or is running too damn rich. If it makes the problem worse, then you might be running too lean. Do you have control over your fuel pressure?
Performing these checks should tell you which direction you need to go.