Leak checking in the middle of the night is always fun. I feel your pain. You really only have four options: leak pipe down the well, leak in distribution piping, over use or tired well or booster pump. Im sure you knew these already as you appear to be a very compitent and experienced owner.
Can you give me a little more info on your system?
Well pump size, age and type
Pressure/ reservoir tank size and type
Booster or just well pump?
Regarding well check valve locations: Many submersible pumps (under 5hp in size) have check valve on top of the pump, then industry standard is 1 check valve per 100 or 200 feet of pipe, some install one at top of well but it is really overkill if you have 1 or 2 down the well.
Best of luck hunting the problem down