Is the vinegar supposed to be diluted? Seems like an odd choice since vinegar will make anything in the cooling system that's steel, rust.
One part Jack Daniels, one part purple cool-aide, and one part formaldehyde used to preserve Hitler's brain that we have in the back.
Vinegar turns rust into a different oxide which is water soluble. So the rust then washes out of the cooling system. There are some steel parts in the cooling system, so it can clean them. Vinegar will not react with aluminum oxide. So it may not be that helpful for the aluminum block engine or AL rad. There are probably other compounds/residues that get washed away by a vinegar flush. Who knows.
What if the rust is mixed with oil from a blown head gasket? I've done at least 5 vinegar flushes and my coolant system is still rusty. MA is insane about this and if your reservoir is the least bit dirty, they'll DQ you. The Dang Yamaha uses steel coolant pipes.
Now, this was on my 97 Chevy 350 cast iron block. I replaced all eng cooling system due to rad leak but before replacing I used the Preston radiator flush from advanced auto. I drained, then filled with water and the flush. Let it run for about an hour then let it soak. Did the hour run daily for about a week as the truck wasn't road worthy. Mine stayed in there about a week. The bottle says 6 hours but I think that's more so people don't forget and freeze them in the winter. After I drained, flushed with garden hose til it came out clear. Filled with distilled only. Ran engine to hot, drained, filled with distilled, ran til hot, drained, filled with antifreeze and distilled. Maybe the vinegar isn't aggressive enough. I got a 26 year old engine pretty darn clean. But it took time. Yours is a race bike, so definitely use some caution. But I don't think the off the shelf stuff will hurt it.
Actual red rust? Vinegar will turn rust black and the flush will turn black too. If the flush isn't black when you are draining it, you arent accomplishing anything unfortunately. Replace the res and the coolant pipes? Samco doesnt swap out the steel pipes for silicone?
It does get blackish, but when I took the engine apart after the last round, the thermostat housing was pretty red. The R7 engine has form fitted coolant pipes that come out of the water pump, unfortunately they're steel and no matter what I use, they rust. I've replaced them a few times for this reason. I got tired of scrubbing out the reservoir with a specially melted toothbrush (gotta get the right angle) and just got a couple of them from Yamaha. They never come fully clean! New Yamaha ones are cheaper than a Motion Pro.
I figured you'd be on top of things. Which water additive are you using and how often are you replacing it? So I know which one sucks at corrosion prevention.
Interesting, I know we always ran water wetter with club and AMA. I wonder if AMA had that rule too, and I just missed it? I know I never had any rust that I recall seeing, and we raced water cooled stuff for 7-8 years.