So I have these for changes:
"The 32kHz xtal, is that really an HC49 case, normally they are the watch crystal style." I will check this, I copied the ATmega footprint, smaller would certainly fit.
"The battery holder will probably clash with the headers and dip socket. " I wil move this left to not have the base overlap any pins that go thru the board. How do I get the battery markings on the bottom of the board?
"Are the mounting holes at good spacing, .1" preferably but at least whole mm." Not sure what you are asking here.
"what's the advantage of the mpu being DIP? Why would anyone want to switch from the 1284P to the 644P? " The socket can handle any of the 40 pin DIPs: ATmega164A/164PA/324A/324PA/644A/644PA/1284/1284P I can make SMD version also once I finish the accessory electrical tweaks.
"3.3V regulator & cap" any other inputs on this? It is only supplying current for the SD/uSD.
"uSD connector only" I like the option of either one. Looks like there are plenty of options for brands & sizes: http://www.amazon.com/s/?ie=UTF8&keywords=64gb+sd+card&tag=googhydr-20&index=aps&hvadid=3806787621&ref=pd_sl_3v9txqilg_b
"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?
"The pressure's on Crossroads" No pressure, I am having fun solving this puzzle.
"Somehow I don't think he's connected anything up yet." Not true - board as shown is all routed. I just rip up small areas and make tweaks as I go.
Real time clock - is any one familiar with this Pericom part: PT7C4311WEX Digikey has them for 85 cents in qty 1, having some trouble locating the datasheet for it.
"One of those chips is extremely fine pitch. I have a similar project and the stencil just came in. I'm pretty nervous about being able to assemble it with a stencil and an oven, never mind hand soldering."
The FTDI chip is really nice for USB. I think that is the only part I'd be uncomfortable hand soldering, the 0805 size Rs, Cs, LEDs look do-able.