Paul - great, fantastic! And big thank you for the photos, as they tell the story best. I am glad you went for it, and it wasn't as hard, right? Actually pretty straight forward.
Looking at the photos, you have quite a lot of junk in those cases. Looking back, I was quite lucky with mine as it was actually very clean in comparison.
Kawboy already answered about the plastigauge. It is also all explained in the manual. You will need everything very clean. Then place strips of the plastigauge on the shaft journals, do not turn it!, and bolt the bottom case as per order in the manual. Then remove all and check - the service limit is 0.11 mm.
Check the markings on the crank case. I couldn't make it out from the picks. Those marks are either '0' or no mark. Also, any markings on the shaft counterweights? Pairing these would tell you preliminary what bushings you have installed. Checking with gauge would confirm. There is a table in the manual. Double check the chart - if anything has changed you will make new pairs and there will be a corresponding proper thickness bushing for it (they come in three colors - three different thicknesses).
If all is within limits, if bushings look good without any heavy scuffing, I would reuse them - they would need to go back in the same journals. I'd even probably rotate them if let's say one side shows more wear and the other little or none.
In my case, since all is mismatched, I will need to go through all that and check if my case and shaft pair confirms (0 - no mark), and see if the correct per manual bushings will be fine. I might have to adjust it, and if anything would be out of range I will need to match the right bushing individually. This might be as well in your case, but like Kawboy said, probably not. You are also in a very good position to have everything matched per factory. So it's mostly adjusting the gaps.
The connecting rods - I'd say if checking the play on them and side travel shows good, I would just keep cleaning all the oil passages through all the holes, to flash anything out. Then oil them well. In case you'd still want to remove them, then a similar process with the bushings. The manual says 'do replace all the nuts and bolts'. That would be ideal. I think they might be available. To be honest, I am sitting on a fence with this. They do look good, but that is of course subjective. The manual is written for the best possible maintenance scenario, with the worst possible outcome in mind, also keeping in mind any dealer made repairs for warranties. On a high performance running an engine at 14 rpm, I'd definitely just replace them. On the other hand, years ago reused whatever was available back in Poland when rebuilding bike basket cases. There was not much available and if it was abroad, the costs were prohibiting. I think people's salaries were about $20 a month in the 80's? I half liter of vodka was $1 on the black market, and maybe 25 cents at the government price? So yeah, bottom line was people cold not afford sourcing a $5 nut. For my bike at the time, a 1956 500cc AJS, I had a machined for a common car at the time called Warszawa. Those decades old parts were re-used, the connecting rod bolts - yes. And for the most part, when people did that - it worked. So really, I'd say at the end we'll have to make an individual call. I wonder what route will you choose.
I'm not an expert and never try to sound like know it all, despite sometimes strong opinions, but mainly using common sense with some experience and background having studied these things at the university (Merchant Navy Academy, engineering - official title was Maintenance and operation of marine power plants, which ranged from pure academics like descriptive geometry etc., theory steel structure, durability and structural stress in materials, and all sorts of specific subject related to engines, compressors, boilers etc.), plus a few years as a tow motor mechanic (mostly forklifts, lots of hydraulics there). Never been a car or a motorcycle mechanic. So, back to those bolts, in my case I will make that call when the time comes, based on what I will see up close, availability and price.
Good to see pages 100, 187, 316, 317 in the manual.
