Ah, so you didn't put together the bottom end yourself? I'm a bit more worried now.
Again, don't want to upset/scare you but if this was my car/engine I'd be very much motivated to take it out for a complete stripdown and re-assessment. A couple of the crank journals look excessively ridged and I notice some of the bearing shells show signs of different wear patterns near the joints, which is a classic sign of something not being right (oval conrod and/or wrongly sized shells/crank journals).
It might be the case - as you say - that it didn't in fact get new bearings. In that case I would be wanting to get the crank journals polished and accurately measured and reground if necessary, the conrods resized and correct conrod and main bearing size grades selected and installed. I think it looks excessively dirty for a newly built engine too. Block/crank oilways not properly cleaned prior to assembly?
Hard to comment on the noise that you are asking about. It could be so many things. I've even seen wrongly-selected thermostat housing bolts (too long) causing a tap tap tap on a top end. But quite apart from the unidentified noise issue I think the photos of the bottom end are - regretfully - worrying enough to recommend full strip down and investigation. Sorry.
If you need any stock replacement parts, please don't hesitate to ask. I've got a garage full of 'em. Would be happy to help if you find anything you need to replace. Good luck!