>>So the question becomes; what controls the folding and methylation processes?

That's an entire field of study right there. As a lot of those changes happen as an animal it taking shape, the work tends to be in in developmental embryology. For a fascinating tour of how this interconnects with evolution, check out "Evo-Devo" (evolutionary developmental embryology). For a spectacular tour, check out Sean Carrol's "Endless Forms Most Beautiful". If you can, try to get the hardbound version, just for the amazing illustrations (I get lost in that book a couple of times a year). It was written before Epigenetics were well understood. For that, pretty much anything by Nessa Carrey (or just watch some of her lectures that have made their way to youtube).

I know approximately nothing about Orch OR. Will look into it. As far as I know, tubules are important for neuron structure and pathways for motor proteins to drag ATP from the main body of the cell, where the mitochondria are to the distal end, and ADP back. The entire cell needs to be constantly pumping ions as a signal starts as some local 'valves' opening up, which in turn trigger the next one on down the axon. The brain using 20% of our energy makes loads of sense when you realize how energy expensive keeping cells ready to transmit signals is...