finally got home to mess with the board, plugged it in fired up atmel studio 7 and no chip ID.. huh. OK so basic troubleshooting begins.
Check the custom made jtag cable: check pinoit is indeed correct.
Notice the board is getting a little warm : no biggie could just be the super charging..
Board is getting hotter still : look over the board for pin 1 markers BLAH! shift registers foot print is off by one pin the whole way around....
So snatched the shift register off the board and bingo chip ID. So I have made all the required changes in the schematic, connected ground to the super.. pin designator on the foot print was backwards. Went to a 6pin jtag that's still compatible with the current cable. Now I'm getting ready to re spin the board.
While the boards are out for fab I'll start validating the rest of the boards communications between the temp sensor and the rtc.
I have already verified the super charges properly and the system switches over to the super when all other power sources are gone.
I'll update again after validation.