I was able to get most of the scratch out with 2500 grit wet/dry.
Despite removing the case.I couldn't get the seals properly aligned in the cover. I ended up leaving them both flush with the case. Both seals were fully riding on the journals. My only concern would be the possibility that crankcase pressure could force them out. This happened in my Honda Prelude. Honda actually added an insert in a recall to prevent the cam seal from popping out.
Also using a small yogurt container cut to size to slip the seals over the crank and intermediate shaft was the only way I could get the intermediate shaft to slip on easily. Trying to install the cover over both shafts at the same time would have otherwise damaged the intermediary shaft seal.