Hi,
Useless answer (sorry) (I use the word "you" a lot, but it's referred to me, you, anyone - "you" as in "one"):
1) Why can't you drive the high-side MOSFETs from the stepped-up/charge-pumped voltage? Could you use an amplifying transistor to boost the MCU PWM signals? I admit I don't understand/see what you're explaining.
2) If the battery is only 3.7V, and you'll let it discharge to 3V at most, then I doubt there is - yet - in existance an LDO that can go that low r.e. drop-out voltage, so either 2.7V MCU supply with boosted outputs, or as you say a buck-boost through an LDO - I'd try to implement the latter, not sure how much important/problematic switching noise, if any, slips through the LDO 'though.
3) Current sense/shunt amplifiers make things a lot easier (so long as output offset isn't going to be higher than the lowest current you need to sense - I "got my fingers burnt" with that issue!).
A great deal of this, referring to question 3, without expert input to give sager and more useful advice, sounds like putting off starting, David, get on with it and find out what's right and what needs further development: you don't know till you try. Again, my test circuits have to be built in stages/subcircuits because each subcircuit is a world of learning that can be effortless and take a day or two to prototype and have correct quickly or more usually a slow, painful month of seeing I haven't understood some of the theory I thought I had, need to read up on a "tiny detail" that expands into a whole new area of needed knowledge and have to go back to the books for another month and keep trying until the first rubbishy mess works as required, but until I've actually tried, the theory always theoretically will work as expected...
Testing rough versions is good as DMMs and oscilloscopes can teach a lot quicker than too much research - real live number facts show where you need to review/re-design a lot quicker sometimes, as you know.
What is ADD? Anyway: Focus, dude - what is necessary that you must do now to get to the next place in the project? If you focus on everything at once without focussing on anything specific you will jump around and get nowhere and not know where to start. Choose a point and stick to that one, make a checklist of circuit parts and until each is "done" don't let yourself get distracted. I like reading, but I have to control: "Oooohhh, that's an interesting topic..." otherwise nothing gets finished, or finished several months later...
I admire you, you've taken on what looks like a little project, but it's obvious that it's actually a big project with several circuits and complex concepts rolled into one device, that you have to fit together, so I wouldn't worry if it's taking time for all the parts to fall into place - all good things in time, and fools rush in where angels fear to tread..., eh
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Sorry I can't offer any practical electrical advice.