With the different threads it does seem to me (first time that I have done anything like this) that whatever was lying around in the factory at the time went on to the bike!
No, not really, it's just that a greater variety of thread forms were used by British manufacturers at that time (not just motorcycle manufacturers) and with the adoption of metric thread forms it can seem a bit odd to some people to find so many different types of threads used.
The metric bit is that one crankshaft main bearing is imperial and one is metric,
Well, metric bearings were not that uncommon on British bikes of the period (Norton Commandos etc.), and your Triumph's wheel bearings are metric too.
the whitworth bolt is the centre 9th cylinder head bolt on my model.
I can't find any data on that thread although I think the other head bolts were still cycle thread at that time?
Any thoughts on why one side of the engine has little compression and what I can do to check any potential problems?
It's difficult to say based on what we know, but it's got to be something to do with the valves or rings, so I can only suggest you check the obvious things such as a broken ring, leaking head gasket or valve not sealing properly?