I may be able help with one item on your list.
This PID algorithm appears to include mode (myPID.SetMode). If mode works with this implementation the way I've seen it work with other implementations (the way it should work) you can use it to "turn off" and "turn on" the PID loop.
Setting mode to manual should...
- Leave the output value at the current value
- Stop updating the internal values from the input
Setting mode back to auto should...
- Reset the internal values
- Provide a "bumpless" transition from the current (old) output value to the next (new) output value
- Seamlessly resume calculations
Good luck,
Brian