Help! Gear noise resulted in temporary front wheel lock-up.

What is your question?

My 1999 Acura RL (3.5L) recently had a used engine swap and upon reassembly the car developed a gear grinding noise that sort of came and went. It definitely changed with the rotational speed of the car and not the engine RPM. In fact, it even happened when the car was put in neutral when rolling. My 1st exception is I believe that it is unrelated to the engine. Yesterday after only about 75 miles after the repair and this sound coming and going, the car violently came to a stop when it sounded and felt like a set of gears broke apart. The car was still running after that scary stop which confirmed that it wasn't the engine. It actually was still drivable after that as I nursed it home. The transmission still seemed to shift through all its gears smoothly. So the tranny seems ok. The mechanic is attempting to claim innocence as his job was to just swap the engines which he did by dropping the engine and transmission out of the bottom of the car. The only thing that seemed strange to me was that he used the original old splined right side axil instead of using the axil that came with the new used engine. My thinking is that why wouldn't he use the splined axil shaft that was already "worn in" with the replacement engine drive differential (final drive?) it came with? I'm wondering if the noise I was hearing was the meshing of the two dissimilar gears from two different engines and most likely from two different year cars. My concern now is what froze up that caused the car to lock up the front wheels and what needs to be done to rectify the situation. The gearing I am talking about is located in the oil pan of the engine. Is that engine oil or are those gears in a separate compartment that is fed transmission oil? How about any metal filings that may have been created as a result of improper gear mesh? Ouch! I could be way off on my diagnosis what else could it be? Your advice or a post on the Acura forum is welcome.