Read 14 CFR 61.160(a)
You're probably not eligible for an R-ATP if "struggled at the boat" translates to: "a person who has been removed from flying status for lack of proficiency or because of a disciplinary action involving aircraft operations"
In this context "flying status" was not intended to include NFO.
Also need to ascertain if NFO Rag Instructor counts for mil comp CFI, not sure about that one. But you need to get it right, if you BS your way through that and some FSDO local-yokel signs you off it will likely come back to haunt you in spades someday if the FAA ever catches on. Don't want to get all your certs revoked after you get a major airline job.