We have two individuals and two LLC's as borrowers. The individuals represent both LLC's. For GMI purposes, do we collect GMI and report the individuals or does it matter as all four are borrowers?

IMO, whomever is listed as the primary applicant should have their GMI reported. Then you have your choice of which of the 3 co-applicants you report. ETA: yes, whether you report the individuals' GMI or not, it still must be gathered (assuming you had a face to face application).

More to it. Originally one of the LLC's applied as primary, loan finalizes three months later with the second LLC as primary, instead. Report original LLC at time of application or report second LLC as on loan agreement on HMDA LAR?

Sounds like you have an amended application (or at least, you should). I'd report the GMI for the 2nd LLC as the primary applicant and then whichever co-applicant is listed first on the application.