Thanks for the feedback, guys. I'm going to shoot for ordering boards tomorrow.
It sounds like booting from system memory or embedded SRAM would be rare cases used primarily for recovering a bricked system. If that's true, I think it would be okay to forgo jumper headers and pulldown resistors. Solder jumper pads should be fine. BOOT0 would be soldered to GND while BOOT1 would be soldered to neither.
Here is the old and new schematic diagrams.
Here are the old (left) and new (right) footprints. For BOOT0 to be connected during the solder reflow process the solder jumpers must be on the component side of the board. To have the jumpers on the back side we could run a trace between the two pads. to reconfigure the jumper a person would need to cut the trace first. If this option is taken, we should add a note to the silk screen, so a person doesn't solder a short between VCC and GND.
I mainly have the MIC5219 there is because it's what I happen to have used in the T400 and I have a bunch on hand. I've tied the enable pin to the input, so it will always be on as long as the is voltage on the input. I'm open to swapping it with the LM317. I'd like to see how the battery circuit and sleep current draw shakes out first though.
SD card inductor
Do you have a specific inductor you would recommend? I haven't used any, so I don't have something to drop in. If you don't have a recommendation, I might leave that for the next revision.
It would be tough to get another 0.1" header pin in that area. I might move to a smaller header for that. Do you experience the connection issues a lot? I usually use just the SWDIO and SWDCLK pins without issue. Maybe I'll just put the NRST pin in a different spot where I have room; they don't all have to be inline.
I'll add 100 ohm resistors to SWDIO and SWDCLK. I will remove the pullup resistor from NRST.
Maybe I should rout it to the breakout header, so it could be connected to a reference on the daughter board. Thoughts? Otherwise, I'll leave VDDA connected, so I can play with using it as a reference as I learn.
I'll toss in some bulk capacitors.
I'll learn more about USB. For this revision, would the circuit work as-is?