I agree that you'll need to change your sand. I had new sand in my filter when I did the conversion. I too waited till the end of the summer and changed the sand after we drained the filter for the season. There were marble sized clumps of some gummy green/black stuff mixed throughout the sand. No more time than you have left in the season, I'd probably wait too, but definetely do it before you start up next year.

Congratulations on the conversion! I can now run my pool for 4 months using bleach & stablizer for what it cost me to just use Clear Comfort for 3 weeks...though I'm more happy about having clear water all the time now.