What did I do now?

Ok, so now the electric start clanks, but the kick start does not produce a noise?
 
Well then, we've narrowed the noise down to the electric start. The starter itself has no parts that could possibly produce this noise, but it is attached to the crank shaft on the left side of the engine via a chain. When chains go loose they have a tendency to slap things, like your stator cover.

If you want to explore, I would pull off the stator cover and see if the chain is loose or if the guide is worn or missing. If you take the side cover off the engine there is a chance you will need a new gasket, however.

There are also a few other guides and springs to look at in there.

http://www.cmsnl.com/yamaha-xs400g-2-special-1980_model8758/partslist/B-11.html#results
 
Well then, we've narrowed the noise down to the electric start. The starter itself has no parts that could possibly produce this noise, but it is attached to the crank shaft on the left side of the engine via a chain. When chains go loose they have a tendency to slap things, like your stator cover.

If you want to explore, I would pull off the stator cover and see if the chain is loose or if the guide is worn or missing. If you take the side cover off the engine there is a chance you will need a new gasket, however.

If I want to make sure my other issues are resolved first, will starting with kick start and riding short distances make the problem worse?
 
If the problem is a loose starter chain, probably not. It sounds, to me, like using the starter is causing the chain to slap.The starter has a clutch so that the engine rotating does not rotate the starter, only the starter can rotate the engine. Ergo the chain shouldn't move unless you use the starter.
 
What issues are left?

Well, it's raining out so I won't take the bike out right now.

I need to verify that the loss of power issue has been resoved ((so far can start on single plug both sides again, but that didn't last long last time.

Need to verify the fuel isn't leaking into the air filter (floats were wrong, and one was getting stuck open. Cleaned it up and fixed the levels.

that's about it.
 
there was a broken metal tab fragment inside my stator when I took it off. It would sound like a metal cough when I kickstarted the bike. After I took it out no more noise...
 
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