Ok, I've put in a whole bunch of time modeling Eclipse/DoT rotations over the past few days. Current findings are basically contained in my modified version of WrathCalcs, posted here:
WrathCalcs - Moonkin DPS Spreadsheet .
Most importantly, I seem to be finding that constant DoT refreshing, regardless of the Eclipse cycle, provides better DPS than the currently accepted DoT behavior of only refreshing during the Eclipse ICD. I have a hunch that better yet still would be refreshing at all times except during the final X seconds of Eclipse, but this is tricky to model well.
In any case, I think we may have been somewhat underemphasizing high DoT uptime in lieu of complete Eclipse maximization. Tinker with the sheet with your current setup and give any feedback. I'm going to work on trying to model the more detailed cycles soon.