Last night I installed OS X 10.9.2 on a second partition on the SSD, so absolutely nothing else could interfere. Wake issue showed up even during the first login setup process. Given the reports of Win7, Win8, and OS X issues, it does seem like an issue with the disk and not the OS.
I’m going to schedule a call with Apple and I’ll update here, just in case they have any suggestions now that I’ve got a bare install to play with.
