Just some thoughts.
A lot of it should have settled by now. Most of the wearing in would have already happened, but its a continual process that will take more riding. The type of oil you run it in with should be a mineral oil without friction modifiers, otherwise it won't run in properly.
Is your compression gauge one for a car (with a long or fat hose) that won't read correct for a bike? It could be that your compression readings are actaully ok, but your gauge is not reading accurate for the bike, so bear that in mind. There are threads on the forum about this.
The flake in the oil, then no flake on the 2nd change is normal and expected, but you shouldn't be consuming much oil. You only mentioned a 'bit' so if its truly just a bit, then everything is normal & the lack of oil consumption will continue to improve as things continue to wear in.
I've done the same as you, now up to 3000kms. I have no oil consumption at all. I just run 20W50 mineral, but i broke it in on 10W40 & even then it didn't use much.
I'd say give it another 1000kms and re-evaluate what its drinking oil wise. If possible, get a mate to ride behind you and see if he can see much smoke coming out of your pipes when you ride (coast) normally. There shouldn't be much, and after another 1000kms, shouldn't be anything at all.
Does the bike feel good on compression when you kick it over by foot? When giving the bike some acceleration, does it feel like it has a good bite when you give it some? A rebuilt motor that has just worn in should feel like it wants to go if everything is reasonably tuned.
Re the valve job, you have new guides, so that is good. Obviously you must have installed new valve stem seals as well, because if not, then that is also a source of oil consumption. The valves should be lapped in at a minimum with valve lapping paste, but if the valve face and seat are not reasonably married to each other due to new valves, then the valve job mrieck mentioned is to cut the valve seat at various angles to marry to the new valve. This is done first, then followed up with a valve lapping job.
I'd say keep riding it & it might continue to improve (& just check your compression gauge for bike suitability). You may have nothing to worry about.
PS: Its good that you didn't let it idle much.