Sep 17 03:23:33 mac kernel: Wake reason: RTC0 (Alarm)
Sep 17 05:12:29 mac kernel: Wake reason: RTC0 (Alarm)
Sep 17 07:01:25 mac kernel: Wake reason: RTC0 (Alarm)
Sep 17 08:50:21 mac kernel: Wake reason: RTC0 (Alarm)
A few minutes ago I decided to take mDNSResponder and mDNSResponderHelper from my mavericks install and disable discoveryd again. So far it seems to be working well. Keep in mind I still have -DisableSleepProxyClient in the mDNSResponder.plist.
I copied /usr/sbin/mDNSResponder* from mavericks to /usr/sbin in yosemite. I then copied com.apple.mDNSResponder*.plist from mavericks /System/Library/LaunchDaemons to /Library/LaunchDaemons on yosemite (I don't like modifying things in /System if I don't have to). Make sure to copy all files using sudo.
I don't have a Mavs install. Any way you can share that file? I also had to revert this fix and now get wake ups every 2 hours again. Would love to fix it as it is constantly ejecting my external HDD's (and slowly driving me insane).