The article was apparently published 8 years ago. Any resolution fir any of these things as yet?
There has been some whittling away at some of these. The Pioneer anomaly was explained by a minute re-examination of the mass of the device. 3 of these items point to the same thing: that the speed of light is not a constant. I don’t think that’s such a big deal, because Einstein was pretty straightforward in saying that it was an ASSUMPTION he used in coming up with his theories because it was based upon the best available evidence at the time. But that is no longer the case, so there is likely to be a correction factor in physics in the future. Instead of E=mC^2, you’ll have E=m(C(X)^2) where X is some kind of fancy function. Since C shows up so much in physics it will have wide ranging implications (like the fine structure constant, for one thing).