Is it possible to only flood one rotor?
 

The motor runs on the front rotor well enough. The back rotor periodically will fire, but generally does nothing.

Yes its possible, two injectors service the rear rotor, two service the front rotor. If one injector is out of whack you could have one rotor flooded.

I would doubt flooding is your issue though, look for bad ignition first.

you are correct, it was the ignition...Though I do not know the root casue yet.

I am using a GM style MSD 2 tower coil for leading plugs on a waste spark setup (not using trailing at the moment). I loosened my rear plug wire on the coil without fully pulling it out and the back rotor came online. The wires and coil were purchased (new) about a year ago, and have not seen much action as the car has been dormant while being worked on. I thought I might have some sort of build up on the contacts so I put some of that dielectric silocone grease in all the end caps on the plug wires. This seemed to do the trick for a while, but I am still having intermitant operation. Sometimes the engine will still run on one rotor, but sometimes its the front, and other times the back, other times it runs on both rotors. I was also having some issues with my dry sump oil system backing up and 5hiting oil into my chambers (very dangerous I know), and we continue to have fuel mixture issues since our ECU has not been fully configured yet. I think we will be able to fix all these issues with a little time though, so hopefully the thing will be running decently in a couple weeks.

Thanks for the help farberio.