My rebuild with around 7k on it was apparently running (for more or less) on one rotor... since the front plugs arent brown (still clean) and the exhaust port on the front rotor is clean...
My question is .. do I need to let the front rotor catch up with the rear before I push it....?

 

As in make sure both rotors have seen at least a few thousand miles? Not sure exactly but I would assume that yes the front rotor would still need to be broken in. More importantly why wasnt the front rotor firing?

 

It was, the problem is a cap was missing off of the primary front injector causing the front rotor to flood while the back was doing all of the work...(this is just a guess)

 

Assuming the front has turned as many times as the back, the seals have made as many passes as the back, and are thus broken in about the same as the back. Just because the front may or may not have been doing the work of combustion, doesnt change the fact that the seals are still making their normal motions. IT is this sweeping motion across the rotorhousing surface that provides breakin.

You need to check compression and make a comparison...if one is drastically lower than the other, there is likely a problem inside. You could be interpreting your results backwards...the rotor may not be doing it's job 100% and the plugs/ports be clean because of a compression problem, not the other way around.