You have posted the Lionel TMCC number for the locomotive, what's the real number.
Pennsylvania LionMaster TMCC 4-4-4-4 T-1 Duplex #5514 SKU: 6-38020
Could we perhaps really be talking about this one?
Pennsylvania LionMaster LEGACY 4-4-4-4 T-1 Duplex #5511 SKU: 6-11207
I wouldn't start replacing $110 parts until I was sure that was the problem. Since this is obviously the Legacy version, the adjustment of the Cherry switch is pretty critical, I'd revisit that. The smoke chuff stopping suggests that it's in the locomotive and not the IR link.