With what you have told us it’s hard to know if we are chasing a charging system problem, or if the alternator is simply undersized for your electrical loads. It’s hard to go much further until we know the total power requirements for your aircraft to compare with the output of the internal alternator at a given RPM.
As per my last post, check the amp draw (as displayed on your G3X) with all airframe loads ON and all engine systems (including fuel pumps) OFF. Then, add that number to the published engine electrical load (8 amps) and that’s your total connected electrical load. Then it’s a simple matter of comparing that number to the alternator output graph to see at what RPM all loads are covered. For instance, if your total connected load is 14 amps, then you would expect your amp meter to go negative below 3000 RPM. If this exercise predicts what you are experiencing while flying, then the single internal alternator is likely too small to keep up at lower RPM - a design issue.
As far as your question regarding the two yellow wires from the alternator, it might be easier to remove the entire connector from the regulator, and test the yellow wires while still inserted in the connector housing. These continuity and insulation tests are done with the engine and all power OFF.