I'm updating using my phone I will resize the images when I get to a computer.
long story short, the boad is alive. With a few mishaps, the voltage switching circuit has a EN pin that needs to be pulled low, not high. This has been fixed and I can now talk to the DS1337.
Serial is up and running, it's a bit finicky. The clock also seems to be a bit off, both the internal 8MHz and the external. Setting the baud rate to 115200 seems to communicate one baud selection below that.. sometimes it works at the selected baud I'll have to hook the clock to the scope and see what's going on.
There seems to be something funny going on with my interrupts and sleep modes as it will go to sleep and wake up only a few times then go for a toss.. either the heap is crashing or the clock is too unstable.
I have not tested the temp sensor yet as I have been fighting with the rtc and the power rail management.
The gist of the power management system is, that when powered from usb the lipo and super cap charge. When unplugged the system switches over to the lipo and the lipo makes sure the super cap is fully charged. If the lipo falls below operating voltage then the super cap kicks in to power the rtc, as the rtc has no battery backup. The super cap should keep the DS1337 running for at least an hour or so before it dies if not longer I have not yet tested the length of time it stays alive.
Due to space restrictions in the program memory and ram I may switch to an Atmega 328. One more board spin should knock all the bugs out.
Need to recalculate the crystals load caps, that may be the issue. Or I may just go with a 37KHz crystal and do some funny clock jumbling to keep the power down.
I'll post more soon.