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The new info you have given seems to have brought the issue back full circle to the disc "surface conditioning" rather than warping. It's a pity the hard braking or "Italian tune up" exercise didn't work but I could only advise persisting with it as there is nothing to lose provided it's done safely. (i.e. check your mirrors before braking on a straight empty road.)
I would recommend having the pads out and scrubbing them as clean as possible with a tooth brush and clutch and brake cleaner, then returning them to their original positions with a little coppaslip on the back. Make sure the pins are clean too. Also clean the discs with clutch and brake cleaner, just a soaked rag will do, but keep turning the rag to a clean bit.
I am sure that if you persist with this that the problem will resolve, you do sometimes have to stick at it. I am now in the habit of wiping my discs very often, especially just after a wash to make sure the discs are dry all round and free of any wax products from the wash/wax. Clutch and brake cleaner is hygroscopic so it works well for that.
It's not a bad idea to just push the pads off the discs if you're laying the bike up for while, such as Winter. I don't think I've ever bothered, but then I gently heat my workshop, so I shouldn't get any condensation in there.
One disc on my 750SS has a slight measurable warp but it is less than the movement that the bobbins allow and so they deal with it. I can feel no pulse through the lever or otherwise.
Wavy discs have the same area of contact by the pads at any given point otherwise they wouldn't work. Twin disc setups are staggered to negate any possible variation in this and give better balance. My three wavy discs work absolutely fine and have done for years.
For what it's worth I find Organic pads to be far better for feel, power and disc life. I haven't used a sintered pad on a bike for about 30 years or more.
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