Tommy, I applaud your positive attitude and response to opinions and suggestions...it's hard to diagnose engine issues without having 'eyes on' and parts in hand and we all have opinions.
Overheated rod small ends usually have oil baked on like your one piston dome and ring lands, your pictures don't indicate this. Were the wrist pins nice and silvery as when new or were they discolored from heat...just a follow up question.
How does the top end look? Were the rocker boxes nice and oily inside? How about a picture of combustion chamber side and rocker box side. Not sure about your comment on blued back side (face?) of intake valve. Any possibility of a picture of the valve?
Is your oil tank stock or chopper style aftermarket? When you cleaned the tank were you able to see bare metal all the way to the bottom? Years of accumulated sludge is hard to remove but could be softened and loosened and ingested by a new engine build. Chopper style tanks often don't have the same size oil restriction hole on the oil return side which limits oil supply to the top end hence my questions about 'nice and oily' rocker box internals and condition.
.0048" piston clearance sounds about right and a cleanup hone job wouldn't change that much...would be nice to use torque
plates to do this but many many have been done without. The cylinder shop should be familiar with older engines utilizing soft iron rings and use the appropriate stones etc. After cleaning the cylinders with hot soapy water, scrub them clean with paper towels and ATF until there is no indication of black residue of any kind, then do it again with fresh paper towels and ATF. Before this final cleaning make sure the cylinder bolt holes are clean and free of any crud also. Make sure rings are oriented per ring install instructions and that they have the correct end gap and if you have to file the rings be sure and deburr the ends and clean the rings to remove any abrasives from gapping.
I'm still thinking the main bearings are suspect by the condition of the drive side main in the pictures...especially if it was new 300 miles ago.
Did you remove and clean the sludge trap on rebuild?
Tommy, I don't really see any big problem here that a clean rebuild won't solve. The wrong cam followers located as in the picture shows that you need to follow the Triumph Manual
more closely on reassembly and you already know the followers need to be either new or reground for use on a new or used cam that they weren't previously mated with.
I think if you had broken this engine in correctly with the stock carbs and settings we wouldn't be having this discussion but due to what appears to be dirt/abrasives damage, I think this engine wouldn't have lived up to your expectations. Now this is just my opinion of course and I'm far from an expert.
Stick with it and you will end up with a nice fun bike with the best looking engine in the business. Mark R.