Here's the paper (I think). It's not in any refereed journal that I can tell, nor can I find any citations to it, or peer review:
http://xxx.lanl.gov/pdf/0708.0681
Nick... yikes! Your questions are the kind that should be discussed over a good beer!
Here's the cliff notes version, though...
Energy "lost" from friction CAN be measured. The energy goes into heating up the environment (making molecules move faster), and can be measured as a change in temperature, as in a calorimeter. (Measure the temp of a glass of water, then stir it, and the temp goes up. Just a tiny bit, but measureable, Joule first did this.) Not circular reasoning at all.
Black Holes do get more massive as they "eat" stuff. And yes we can measure how massive a Black Hole is (by the orbits of things around it). We can't measure its physical size, because that is inside the event horizon. Doesn't mean it isn't getting bigger in there.
The Hubble law: (speed that things are moving away) = (a constant) * (how far away they are).
The explanation for this is that the entire universe is expanding. If true, nothing should be moving closer to us.
Of course, for nearby objects, the speed that they move away is very small, and can be overwhelmed by local effects, so nearby objects can be "blueshifted" rather than "redshifted". The Hubble law only kicks in measurably for stuff at very far away (or "cosmological") distances.
The Uncertainty Principle doesn't say that *everything* in the universe is uncertain, just our measurement of a particlar property for a particular single particle. Constants of nature (like the speed of light, Planck's Constant, etc.) are measured very accurately, using many many particles. The Uncertainty Principle is a very precise statement actually, derived from a very precise theory. (Difficult to explain without more beer.)
In short, I believe in basic modern physics. QM and relativity have been around for 100 years, and are both extremely well-tested theories. Dark energy, on the other hand... jury is still out...
--Kath