No Daz, I don't think your rectifier would be causing this. I'm wondering if your leaning out and starting to run hot. If so, your temp sensor should pick up on this and warn you.
The other thing I'm wondering is if you may be drawing a vacuum on your fuel system by having a stopped up vent line.
You said "oil plugs look normal", I'm going to assume that a typo and it was meant that your spark plugs look normal.
Check your fuel tank for a vacuum the next time you take it out and you start having this problem. Make sure you turn off your engine so you can hear it, then loosen the cap to see if there is a vacuum on it.
If not, then you may want to check your carbs. You don't say what year your GS is, so I don't know if your running single or twin carbs. If your running twin, you'll need to check for syncro.
Let me know what year GS your running.