The three yellow wires will get "hot" ie warm enough to notice. More important is the quality of the connections. Your "wires burning" issue is probably bad connectors due to old age. Replacement connectors of same or larger size will stop the burning. IMHO connector maintenance, best practice thermal mounting of the rect/reg, direct rect/reg to battery connection and headlights always ON running should result in a reliable charging system and a long battery life.

Rewired the charging system with 2.5mm cable, soldered the spade connectors for the regulator, eliminated the connector block, and also ran the negative and positive cables straight to the battery.

I'm now measuring 14.2v at 5500rpm. Hopefully everything is going to be working as it should now.

Thanks guys.

My RVF started running real rough (4000rpm on-wards) on the way home and my first thought was the valve check I have to get done. she wasn't getting there gradually, just started her up and bang, wouldn't pull.

In doing a search to find any issues roughly the same has lead me to this topic wondering if it is electrical.
so I did a reg/rec check and got these readings.

red top left pin, black bottom pin; left 538, middle 531, right 515.
black top right pin, red bottom pin; left 526, middle 530, right 530.

Do these readings justify a dead one?

The battery had 13.4 volts with ignition off.

When I took the tank and air box off I noticed there was what I think to be fuel on the rear head coming from the carbie overflow tubes.

I'm going to take the carbies off to get a mate to show me how to check valve clearances, but should I track down this problem before I go any further.

My next guess would be to check to two cdi? units.

Your rectifier looks ok but the regulator section might be stuffed. What battery voltage do you get at 5000 rpm. A stuffed regulator can confuse the ignition unit resulting in poor running and eventually may cause non repairable damage.

I would fix you current running problem before moving to other issues.