That the thing about dark matter... it has a perfectly reasonable explanation (WIMPs). It's not that weird of a "thing".
I dunno. Usually when a theory requires more and more unseen entities over time it's a sign that it's time to replace the theory. We know General Relativity is incomplete, both because it doesn't take into account quantum effects and because it has internal contradictions - specifically, it assumes a continuous spacetime geometry but predicts non-continuous points (black hole singularities). Most likely Einstein simply missed some observer-specific assumption - for example, GR assumes mass-energy has an exact distribution rather than probabilistic one - and thus GR is not completely general.
A question I've had for a while... if space itself is being inflated (or any sort of mathematically equivalent scenario) - everything inflating in all directions at all scales - wouldn't there be some sort of weak radiation signal from electrons expanding into a higher energy state due to dark energy and then collapsing back down?
No, because a continuous force wouldn't drag electrons up and then let them drop back down. What it would do is alter orbital structure and energy levels. But how they'd be altered depends on how quantum mechanics and GR combine, which we don't currently know.