How do I get the battery markings on the bottom of the board?
Don't know, I don't use Eagle for anything but viewing other people's files.
"Are the mounting holes at good spacing, .1" preferably but at least whole mm." Not sure what you are asking here.
Just that the distances between mounting shouldn't be something like 57.356mm that's hard to measure with you come to mounting it in a box.
"SQW signal going to an interrupt pin so you can create a version of millis() that doesn't skip a beat or have the RTC wake the processor at 3AM. " I think I can do that - does it need to a hardware interrupt like INT2 on pin PB2, or can it be a PCINT like PD7?
Either way, I would probably save the INTs and use a PCI, but INT2 would be a bit easier to use from the software point of view and it's "spare" according to the Arduino or do the 1284 core files handle attachInterrupt(2,xx).
"3.3V regulator & cap"
The MCP1700T is good, @ 250mA it will handle the power I would think, what power do the SD cards draw? The SOT23 has a tempco of up to 336 C/W and the the SOT89 only 52 C/W. So the SOT23 can only handle about 1/3W at room temp (depending on how much copper it has around it).
is any one familiar with this Pericom part: PT7C4311WEX
Not me,it looks similar to the 1307 but I don't see any benefit to using it. The RX-8025 mentioned before looks nice and I do like the built-in TCXO, but if you went that route I'd go with the DS3231 chip. There are libraries for the common chips, probably not for the others, so unless there's a really neat feature not available on the 1307/3231 I'd stick with them.
One of those chips is extremely fine pitch.
I use a hot air gun to solder these (the FTDI is the finest I've done so far), easy, just run two beads of paste along the pads and hit it with the hot air. Clean any bridges with solder wick.