Thanks for the update, Ken!
Hopefully, you are able to make the jog switch more responsive by using interrupts instead of polling.
As for the power circuits, it is nice to be able to use a single 3.7v Li cell with an inverter but in order to get noise levels down (you want a 3GHz top end), using two cells and running 7.2v through a low noise analogue regulator to 5V and then to 3.3V will remove most power supply noise.
The down side of 2 cells is requiring >8V for charging the batteries (and price) although with really good filtering, the unit can still be powered from the USB port.
Just some thoughts...
Larry