What is the appropriate type of CLIN that should have been on contract to resolve issues like these?
Without knowing the details of how the contract is set up, I assume the contract contains a clause such as the one at FAR 52.246-17
that address warranty provisions for the items. Also note that operational procedures for addressing quality deficiencies in the Air Force are contained in T.O. 00-35D-54, USAF Deficiency Reporting, Investigation, and Resolution. A copy can be found here (https://acc.dau.mil/CommunityBrowser.aspx?id=442819
Having pointed out these two considerations, I'm not sure what CLIN issues remain regarding quality deficiency reporting and contractual remedies for the deficiencies, as the warranty clause and the technical order should adequately protect the Government's rights.