U.S. Citizen, NOT a bona fide resident of Puerto Rico. General Income. U.S. based company. ON pay stub. Puerto Rico Tax taken out (6k). Form 1116 Needed?

Suggest you read through Pub 570.  It tells you everything there is to know about filing requirements based on various scenarios, de minimis exception, and applicability of FTC.

It doesn't seem clear from your original post why there was PR tax withheld on the last paystub, what amount of income was reported to PR, and whether taxes withheld were actually remitted (it is not uncommon for payroll to make mistakes, which they rectified after the close of the year even after W-2's are issued, and only if they realize there was a mistake).  Have you established the actual PR liability?  If your client did travel and work in PR, including those for personal purposes, have you reviewed his travel records and workday details (which may include prior 3 years)?

"All I have been able to obtain is information about residents and federal employees."

By your own admission, you don't seem to have all the information on hand.  Until then, you can't really determine the proper filing position.

BTW, I'm not sure what you mean by "federal employees" when your post also says your client was with a US-based company.