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@Gordon
Yes, 10k is fine - however if you use software I2C then there is no need for pullup resistors :) It's still an idea for SD cards though (at least on CS)
You don't actually need to use B3/4/5/etc - on the nRF52 chip you're using you can use any pins.
In terms of RTC, I think you are. The RTC will need its own battery or it will lose time too, so why not just permanently connect a battery to the MDBT42? Even a supercap on the 3.3v line should provide enough power for the main battery to be unplugged for a minute or so.
The MDBT42Q draws so little power it seems there is no real reason to turn it off.
Also you have 40k of nonvolatile storage on the MDBT42Q - so if that's enough you could avoid the SD card. SD cards can draw a lot of power when on so you may have difficult running from a small battery