My Mac has sleep apnea

My Mac wakes up frequently. I mean REALLY frequently, like every couple of minutes all day and all night.
I have the Mac set for wake for ethernet access so that I can use Back To My Mac when I'm at work. I understand that it will Dark Wake periodically, but every couple of minutes seems excessive.
The system is an early 2009 Mac Pro | 2 x 2.26 GHz Quad-Core Intel Xeon | 14 GB 1066 MHz DDR3 ECC | ATI Radeon HD 4870 512 MB
2 connected monitors (24" Cinema Display via Display Port, and HP L2335 via DVI)
There is a blu-ray drive mounted in the lower bay, and 4 internal drives mounted.
Also One USB drive, and one Firewire drive plugged in, but both switched off.
It's hardwired via Ethernet 2 port to an Airport Extreme Base Station (version 7.6.4)
The base station is set to forward calls to port 5900 to this Mac port 5900 (for screen sharing)
I'm currently running OS X 10.10.3, but the problem has persisted since Mavericks I believe. It all did work perfectly at one time in this identical hardware configuration.
After not being able to troubleshoot this earlier, I disabled wake on lan, and turned off port forwarding on the airport, and then the Mac was able to sleep through the night (mostly), but still would dark wake occasionally.
A couple of weeks ago I wiped the Macintosh HD and did a clean install of Yosemite, then migrated over my user account from a backup.
I then had some strange Calendar & Reminder issues that I couldn't solve, so I built a new user account from scratch, and now everything seems to be working fine. (the migrated user account is still on the drive, though not logged in)
Yesterday I decided to see if I could get Back To My Mac to work again, so I reenabled Wake On Lan, and Port Forwarding, and now the Mac will not sleep.
Based on what I'm seeing in the console, it appears that something is triggering the ethernet, but it's certainly not me
If anyone has any thoughts or advice I would be grateful.
Here's a taste of the console to show you how frequently it's waking up. It goes all day and night like this, but this is just a sample:
4/20/15 12:35:56.966 PM discoveryd[75]: Basic DNSResolver UDNSServer:: PowerState is DarkWake
4/20/15 12:35:59.100 PM ntpd[206]: wake time set +0.866042 s
4/20/15 12:36:46.000 PM kernel[0]: Wake reason: (Network)
4/20/15 12:37:12.001 PM discoveryd[75]: Basic DNSResolver UDNSServer:: PowerState is DarkWake
4/20/15 12:37:27.003 PM discoveryd[75]: Basic DNSResolver UDNSServer:: PowerState is DarkWake
4/20/15 12:37:26.936 PM ntpd[206]: wake time set -0.542928 s
4/20/15 12:38:14.000 PM kernel[0]: Wake reason: (Network)
4/20/15 12:38:37.002 PM discoveryd[75]: Basic DNSResolver UDNSServer:: PowerState is DarkWake
4/20/15 12:38:52.007 PM discoveryd[75]: Basic DNSResolver UDNSServer:: PowerState is DarkWake
4/20/15 12:38:53.307 PM ntpd[206]: wake time set +0.481005 s
4/20/15 12:39:40.000 PM kernel[0]: Wake reason: (Network)
4/20/15 12:41:19.002 PM discoveryd[75]: Basic DNSResolver UDNSServer:: PowerState is DarkWake
4/20/15 12:41:33.970 PM discoveryd[75]: Basic DNSResolver UDNSServer:: PowerState is DarkWake
4/20/15 12:41:36.034 PM ntpd[206]: wake time set +1.075099 s
4/20/15 12:42:23.000 PM kernel[0]: Wake reason: (Network)
4/20/15 12:42:59.002 PM discoveryd[75]: Basic DNSResolver UDNSServer:: PowerState is DarkWake
4/20/15 12:43:13.974 PM discoveryd[75]: Basic DNSResolver UDNSServer:: PowerState is DarkWake
4/20/15 12:43:14.499 PM ntpd[206]: wake time set -0.268583 s
4/20/15 12:44:02.000 PM kernel[0]: Wake reason: (Network)
4/20/15 12:47:32.002 PM discoveryd[75]: Basic DNSResolver UDNSServer:: PowerState is DarkWake
4/20/15 12:47:47.840 PM discoveryd[75]: Basic DNSResolver UDNSServer:: PowerState is DarkWake
4/20/15 12:47:48.963 PM ntpd[206]: wake time set +1.046544 s
4/20/15 12:48:36.000 PM kernel[0]: Wake reason: (Network)
4/20/15 12:48:56.002 PM discoveryd[75]: Basic DNSResolver UDNSServer:: PowerState is DarkWake
4/20/15 12:49:11.031 PM discoveryd[75]: Basic DNSResolver UDNSServer:: PowerState is DarkWake
4/20/15 12:49:12.570 PM ntpd[206]: wake time set +0.428623 s
4/20/15 12:49:59.000 PM kernel[0]: Wake reason: (Network)
4/20/15 12:51:37.002 PM discoveryd[75]: Basic DNSResolver UDNSServer:: PowerState is DarkWake
4/20/15 12:51:51.958 PM discoveryd[75]: Basic DNSResolver UDNSServer:: PowerState is DarkWake
4/20/15 12:51:53.987 PM ntpd[206]: wake time set +0.790172 s
4/20/15 12:52:46.000 PM kernel[0]: Wake reason: (Network)
4/20/15 12:52:46.002 PM discoveryd[75]: Basic DNSResolver UDNSServer:: PowerState is DarkWake
4/20/15 12:52:59.176 PM discoveryd[75]: Basic DNSResolver UDNSServer:: PowerState is DarkWake
4/20/15 12:52:59.812 PM ntpd[206]: wake time set +0.356395 s
4/20/15 12:53:47.000 PM kernel[0]: Wake reason: (Network)
4/20/15 12:53:51.001 PM discoveryd[75]: Basic DNSResolver UDNSServer:: PowerState is DarkWake
4/20/15 12:54:04.707 PM ntpd[206]: wake time set +0.715150 s
4/20/15 12:54:04.945 PM discoveryd[75]: Basic DNSResolver UDNSServer:: PowerState is DarkWake
4/20/15 12:55:54.000 PM kernel[0]: Wake reason: (Network)
4/20/15 12:55:54.002 PM discoveryd[75]: Basic DNSResolver UDNSServer:: PowerState is DarkWake
4/20/15 12:56:08.942 PM discoveryd[75]: Basic DNSResolver UDNSServer:: PowerState is DarkWake
4/20/15 12:56:09.803 PM ntpd[206]: wake time set +0.550490 s
4/20/15 12:56:57.000 PM kernel[0]: Wake reason: (Network)
4/20/15 12:57:32.002 PM discoveryd[75]: Basic DNSResolver UDNSServer:: PowerState is DarkWake
4/20/15 12:57:46.973 PM discoveryd[75]: Basic DNSResolver UDNSServer:: PowerState is DarkWake
4/20/15 12:57:48.486 PM ntpd[206]: wake time set +1.022997 s
4/20/15 12:58:36.000 PM kernel[0]: Wake reason: (Network)
4/20/15 12:58:44.001 PM discoveryd[75]: Basic DNSResolver UDNSServer:: PowerState is DarkWake
4/20/15 12:58:57.827 PM discoveryd[75]: Basic DNSResolver UDNSServer:: PowerState is DarkWake

Just spotted this in the console, even though After Effects wasn't running, an the Mac was awake at the time.
4/20/15 6:56:51.000 PM kernel[0]: process After Effects[2260] caught causing excessive wakeups. Observed wakeups rate (per sec): 433; Maximum permitted wakeups rate (per sec): 150; Observation period: 300 seconds; Task lifetime number of wakeups: 82286
4/20/15 6:56:51.068 PM ReportCrash[2359]: Invoking spindump for pid=2260 wakeups_rate=433 duration=104 because of excessive wakeups
4/20/15 6:56:52.876 PM spindump[435]: Saved wakeups_resource.diag report for After Effects version 11.0.4 (11.0.4) to /Library/Logs/DiagnosticReports/After Effects_2015-04-20-185652_MacPro.wakeups_resource.diag
4/20/15 7:02:27.000 PM kernel[0]: process After Effects[2260] caught causing excessive wakeups. Observed wakeups rate (per sec): 154; Maximum permitted wakeups rate (per sec): 150; Observation period: 300 seconds; Task lifetime number of wakeups: 146539

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