If the VR's internal cutout relay is failing to ever close and by pass jumping across it (BAT to GEN/ARM) makes her charge yeppers sounds like a bad VR HOWEVER that assumes shes all wired right and all polarities are correct (genny and ammeter and battery etc). While what you say (that pegged ammeter dont sound exactly right) and my test tends to say that Im still concerned all your polarities are correct because the more common VR cutout relay problem is them sticking closed versus failing to make up.
If the ammeter polarity (and battery) is correct, if you turn on lights or ign engine not running it ought to swing over to - discharge!!!!
Id say the jury is still out