Threading oyur loom through the backbone is perfectly fine provided you don't drill large holes everywhere. A hole at the front and one at the rear is good. Been done before safely.
Near in mind that pipe may be quite hot and you'll be sitting on top of it. I'd certainly coat it inside and out with ceramic costing. And probably heat wrap it too.
Yes, I've been thinking about that, I've also been thinking that after the things you mentioned I may fab up some sort of shield to go around the outside of the wrap, more to shield it from rocks and debris. Again, this is all just theory right now. I ma not even run it that way. I just thought it would just keep a narrower profile to the whole bike.
The other thing I was really thinking about last night was my intake manifold. The goal here is to make as much power out of the stock (well stock replacement) engine. So knowing how automotive engine air intake are designed, I was wondering, just like the argument for pods vs stock airbox vs velocity stacks. Maybe something like this is in order...
