Time to help out with the todo-list
Unless you're planning to add another SWD JTAG device on the board, there's no need to even route SWO. SWO is an output, so you can daisy-chain several SWD devices together, so you can use one JTAG to debug several chips in a system at once.
Yes. Very much so. The STM32 series needs an external cap on nRST, or you can get spurious resets.
Columb-counters are sexy beasts, but they're probably a bit overkill in this application. Approximating SoC (State of Charge) from just VBAT is enough, unless you put loads high enough on the battery for the IR to matter. (In that case, you'll get erroneously low readings when the system is under load)
Have you had any reports on the T400 about SD-cards being unstable when writing to them? As in, system resets or corrupted data/readings ?
If not, I'd probably leave it out.