Okay, I'm calling it done electrically. Gonna work on cleaning up component names next, check availability of all parts, from sparkfun or elsewhere.
Found a little 32K crystal for the RTC. Sticking with the DS1307 as it seems well known. Brought the square wave to the middle of 3 header pins, other 2 go to INT2 and PD7, select your interrupt choice. May change it to much less expensive part (85 cents vs $3.72) if I can find a datasheet. http://search.digikey.com/scripts/DkSearch/dksus.dll?Detail&name=PT7C4311WEXCT-ND Hmm, maybe not - not much flexibility on the square wave out: http://www.pti-ic.com/new/manage/doc_datasheet/PT0322%20%20%20%20%20PT7C4311.pdf 512 Hz only vs http://datasheets.maxim-ic.com/en/ds/DS1307.pdf 1 Hz/4K/8K/32K Hz
Not doing any more with low power operation, wasn't my goal for this board. Figured this to be an actively powered device with the 2 interfaces and the SD card going for whatever reason. Got the battery socket on the bottom of the board, away from any thru hole interference.
Made sure the mounting holes were on 0.10" spacings.
Any Eagle experts out there? I need someone to confirm the pads are correct for the 2 regulators. They look odd to me. PM me with address, I'll send the eagle file.