Hello Jon and welcome to our humble site.
That’s a great history you have there and I feel very positive you have a great bike there requiring minimal effort to make it roadworthy.
Apart from the exhaust and obviously the paint job she does look very much original. That includes the front mudguard as those dimples are where the top mounting bracket is spot welded to the main part.
The tank badge mountings have been filled in when the respray was done. It will original have looked like this
The way you describe the engine also gives me confidence it will fire up without a problem so I don’t see any major expense there however should you need anything I can probably get it for you if I don’t have it already.
Regarding the timing chain that sounds like it is a little tight. When you turn the engine over by hand (Anticlockwise from the points side, yes this engine runs backwards) at the plunger rods farthest out point it should be flush with the body.
Have you got original Mikuni B38 carbs on? If so why do you need a Y piece? Each carb has it’s own line straight from the tap hence 2 outlets.
The last point is that the toolkit did not come with a shim tool. They are available from ebay though should you need one and I have all shim sizes in my stock of parts.
I cannot help you regarding a powder coaters. I have a great one here. I had the frame, swinging arm, yokes and all the brackets done for £120 but I am up north so a bit far to travel.
I look forward to seeing your progress.