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!
So more haste, less speed on my part then. I had set myself a target date on summer 2018 to have the car running on the road and therefore it was my intention to get the original engine running with minimal cost as the rest of the car is costing sooooo much to build. Now I wasn't intending upon the engine being a rattling, smoking disaster but just something that would allow me to enjoy driving the car for a while before then deciding upon what it is I would like from the engine in the long run. I didn't really have much of an option when it came to the head as the original one was too far gone IMO, so I sourced another and put some money into it to make it suitable for the triple Dellorto's I have.
I wanted to drive the car for a while before I decided upon what exactly I wanted from the engine. I'm not going to be racing this car but I do like something that gets going when you tell it but without it being highly strung. One option I was considering was to buy a spare block and have it re-bored or honed, any needed repairs done and then chemically cleaned. Then I could build this block in my leisure, perhaps with forged rods and pistons, according to how I feel about the experience of driving my car and also required funds of course. I have also been thinking about a lot of other possible upgrades, which are all very expensive but I'm really not sure yet if I'm going to need them.
Anyway that plan has now gone out of the window, so I may need to yank the engine out and do a better job of it as the general consensus is that I need to do something with these bearings and perhaps journals at least. I think I shall remove all of the bearing caps and inspect the journals a little closer and get some more photos before I take the engine out. With a bit of luck it might be that I can for now at least get away with fitting new shells and then think about later options.
Thanks for the offer of replacement parts, I may well need some soon.