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CYBORG
I think yours is a good starting plan. Run some cheap orilleys oil in it with a dose of seafoam to do a flush and then run it a while and keep an eye on the sight glass for anything that looks bad. Im just a bit freaked out with seeing that oil

I can understand freaked out. My bikes don't see the road as much as they used to. But I run them up to temp every weekend. Seems to help keep the seals and stuff stay ln shape

So heres my plan. Take air hose and put air in the thermostat housing and listen for air through the oil fill hole to check for cracked water jacket.
If no air sounds im gonna declare the water jacket is not cracked put oil in and fill the system with plain water and run it with some used oil change oil from my collecting jug and then drain it so any trapped moisture is pickup up in the oil then drain it. Then im gonna put in a second batch of new oil and run it till the fan cycles a few times and drain some off to see if that batch is milky. It may be just years of condensation had caused the problem like was mentioned. I sure hope thats the case.

If the bike runs … warm it up … then pull the plugs … the bad cylinder will 'steam clean' its plug

Gord

When i first rolled it out of storage a few weeks ago it started on full choke but i knew the carbs would need gone through. This is when i discovered the starter clutch was hit and miss. So i decided pull engine to fix starter clutch and put in new friction plates. Draining the oil exposed the brown oil and my panic for an explanation ensued.

Pull the plugs and look at them Chuck !

Well i took the thermostat out and taped off the water pump hose. Then taped the air nozzle to the thermostat housing and put the housing back on. Took off oil fill cap and pressurized the coolant system and did not hear any air sounds getting to the crankcase. Thats reassuring. Ill finish getting radiator and all that back on and start it with just water and let it get good and hot till the fan runs a few cycles while watching the exhaust for any steam plumes.
Then ill check plugs for any nice clean ones. Ill report back at some point on how it goes.

Good idea

Fired it up today with just water. New oil and ran till fan came on then drained oil. It came out ever so slightly milky but i expected there'd be some residual gunk in the engine. No wisps of water vapor out the pipes either.
Ill refill with new oil tomorrow after it drip all night. Repeat the process and recheck the second batch of oil and check the plugs. So far it looks like Cyborg was spot on about condensation. More will be revealed.

i get it right every once in a while Glad I was this time

Cyborg, I figured that as long as it ran if there was a serious problem the oil would have been really nasty and it wasnt.

Good to hear it. Time to get it on the road

for what it's worth, and I know some people disagree with this procedure; every 'new-to-me' used bike I've purchased I've run about 4.5 quarts (slightly overfilled) of diesel fuel in the crankcase in place of oil. I learned it almost 40 years ago from an old geezer mechanic.

start the bike (or car/truck) & let it idle to operating temp plus give it another 15-20 minutes run-time at temp.

there are some serious caveats during this procedure;
DO NOT rev the engine.
DO NOT RIDE the bike (or drive vehicle).
that being said, on a GL, I don't think it would hurt anything to use the clutch and run it through all gears.

it seems to work. I've never had any issues.
but I've only done it six or seven times.
the gunk that's come out was amazing on a couple.

once the diesel is drained, put in your normal engine oil/new filter & ride gently for a couple hundred miles. change the oil and filter with new and you're good to go.
I generally don't put a new filter on with the diesel, just run the filter that was on there.

I've been told the detergents and solvent nature of diesel fuel gently scours or scrubs the inside of the crankcase. I don't know.

my .02 worth on engine crankcase cleaning.

I agree. I've done it. And it works