That is a major bummer but very good to hear it runs well now and the mystery is solved. It sounds good and healthy!
There is hardly anything more frustrating (or confusing) than new parts that are defective. Especially difficult to deal with in a situation like yours, in a major overhaul where many things on the engine have been replaced all at one time -- very hard to pinpoint the particular guilty component when there are so many possibilities. Nice work getting to the outcome and thanks for sharing the whole story, it will be a good resource for others in the future.
Pretty sure you can be confident the engine will be fine in the long term, not likely to see any lasting effects from everything that happened. A good hard run once installed in the vehicle and after the initial oil change will certainly be therapeutic for it.
