That's not surprising at all that the junkyard cut the wiring. I had that happen to me also, when I am in the yard with a pick-up truck to pick up the engine myself. I looked at the engine. Agreed to the condition and price. The junkyard told me to go have a cup of coffee and come back. The engine will be ready then. By the time I came back, the engine was ready with wiring cut.
Many junkyard in NY metropolitan area hire immigrant hands from south of the border. This is not a slight to the people there. They are not trained in anyway to do this kind of work nor do they have the knowledge. If they are not closely supervised, as often is the case, you end up buying a heap of junk, or at least a lot of trouble.
'01 540it, 6/01
'03 325i 5 speed, 9/02
'10 535ix. 9/09
'10 mini 6 speed
'15 mini countryman 6 speed