Payment is due upon completion, however wouldn't inspector approval be part of the completion process?
One would think so. Do you have anything in writing to that effect? As an inspector, I have had this kind of situation come up occasionally in the past, and it puts me in a somewhat difficult situation. The issues you describe seem relatively minor, but if the inspector is not comfortable approving the system, all he or she can really do is disapprove the installation because it doesn't meet code, and hope for your sake that the system works anyway. If site constraints permit, additional length
could be added to the shorter lines to satisfy the inspector, but other than that, once the system is in the ground, the "damage" is unfortunately already done.
Again speaking as a regulator, I don't think I would officially concern myself with the details of the transaction between contractor and customer, but you may have some civil recourse that would allow you to keep some of the agreed to purchase price of the system since it was not installed entirely to code.