1. Yes – the main substrates for gluconeogenesis (and subsequent production of glycolysis) are lactate, pyruvate, glycerol, glucogenic amino acids and intermediates of the TCA cycle. Essentially, any intermediates that can proceed through the TCA to make oxaloacetate will be appropriate substrates for gluconeogenesis.
2. Pyruvate is indeed a polar molecule. There are electronegativity differences between oxygen and carbon leading to uneven sharing of electrons and polarity. Because of this, pyruvate will not pass through any biological membrane. But that leads to the question.. how does pyruvate get across the OMM? The outer mitochondrial membrane is actually quite permeable, much moreso than your normal cellular membrane bilayer. The OMM contains proteins called porins, which form channels that allow the unregulated diffusion of large molecules through these relatively non-specific, voltage-dependent anion channels (VDAC), or porins. These porins allow for facilitated diffusion of molecules into the intermembrane space.
In contrast to outer mitochondrial membrane, the inner mitochondrial membrane is impermeable and does not have such channels. The transport of pyruvate through inner membrane occurs by a carrier-mediated process.
Similarly – NADH is permeable only at the OMM via the porin channels. The inner mitochondrial membrane is not permeable to NADH. The solution to obtain energy from NADH is that electrons from NADH, rather than NADH itself, are carried across the mitochondrial membrane.
Ketone bodies are also polar, but the ketone bodies acetoacetate and 3-hydroxybutyrate are organic acids that diffuse freely across cell membranes into the blood and other organs of the body (notably the brain!).