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Have you loaded a flat curve and shot it with a timing light?  Where did you install the rotor timing wise and did you update same in the zeel box for your static timing? This is always step 1 to make sure you have control of the curve. For clocking of the rotor, check your highest point in the curve you're running and make sure the rotor carries at least that much advance.

Nice job on the bike! Look'n good! 

A lot of guys run the 4ah scooter/alarm batteries that connect with spades. They seem to hold up well in a dormant state, which works well with RD's that spend most of their life sitting in the garage. And just let them sit in the bike, no charger. My experience with other typical motorcycle batteries is they all suck and you should plan on replacing them every year or two, maybe 3. Some guys swear by Yuasa but I don't find them to be any better than generic batteries and the Yuasa's have quite a premium price. Like tires and premix or the pump, there's no shortage of opinions about batteries.   

The YTX5L-BS will fit in the stock rd battery box, we've sold them for years. It's a bit narrower but you can block it up with some foam.  I don't think it's going to help with plug fouling, what heat range plugs are you running?

They also can lose efficiency when they age due to brush dust / grime on the contact rings and corrosion of bullets/connectors, loose connections. Gets dirty in there after a half century and brass connectors oxidize. Some contact cleaner on the rings and replacing old connections can help. I've had bikes come in that would only flash the signals if revved, after some good old-fashioned maintenance and a new harness, they'll flash with just the key on. Often mis-diagnosed as a bad flasher relay. 

AI says

Motorcycle generator connections are crucial for maintaining a reliable electrical system, but they can be prone to oxidation and corrosion over time. This can lead to poor conductivity, voltage drops, or even electrical failures. To prevent these issues, here are some tips:

Inspect Regularly: Check the connections for signs of oxidation or corrosion. Look for discoloration, buildup, or loose connections.

Clean Thoroughly: Use isopropyl alcohol or a contact cleaner to remove any oxidation. A small brush can help with stubborn spots.

Apply Dielectric Grease: After cleaning, apply a thin layer of dielectric grease to protect the connections from moisture and oxidation.

Secure Connections: Ensure all connections are tight and properly seated to avoid arcing or further damage.

Protect from Elements: If possible, shield the generator and its connections from water, dirt, and other contaminants.

These work great, plug and play.

https://www.economycycle.com/shop/yamaha-rd250350400r5ds6ds7-parts/electrical-ignitions-lighting/electrical-parts-and-related/regulator-rectifiers/yamaha-rd350-rd250-all-regulator-rectifier/

The 400's have the threaded bolt instead of the roll pin.

We have the VS Dyna ignitions in stock.

https://www.economycycle.com/product-category/yamaha-rd250350400r5ds6ds7-parts/electrical-ignitions-lighting/ignition/dyna-s-ignitions/

Torque the crank/rotor bolt to 15ft/lbs.

Fit them dry and do a leak down test, only way to know for sure. Pressurize to 6lbs, no more than 1lb per minute loss.   

Thank you for your continued support and business Tim, much appreciated!

There's also the option of a reproduction RD MC. It's the whole assembly and lever. They look and function just like the originals and are $85, preassembled ready to mount and bleed.

https://www.economycycle.com/shop/yamaha-rd250350400r5ds6ds7-parts/frame-related/brakes/front-master-cylinder-kit-rd250350-reproduction/

Autocar in the UK now.

https://autocar-electrical.co.uk/newtronic-product-guide

I agree they'll make useable power way beyond the wear spec, especially for street riding.

You're missing part of the equation. what you need to know is the piston to cyl wall clearance, that tells you if the bore is worn. The nominal size of the piston just tells you what bore you're on.