tricky -
so you'll switch motors out of new headlight too (maybe with sellers auth) and see if it new motor inside new unit could be faulty, and maybe try new motor in old L body. ?
but, maybe, diagnostics on left light get supressed if there is fault on right, so left has another problem on top of motor (connectors yes - but seems weird if aforementioned connector can't be provoked into failure by wiggling)
would be nice to get your hand on ford diagnostic manual, if it has hints, but, as you say, additional diagnostics/secondary boot loader might be needed.