Yeah, I have to agree that the board isn't the neatest and with those cheap cables you are prob getting alot of tone loss as well. The shielding on those cheap chinese jobbies are terrible and also running your power across your audio lines like that isn't very good either.
This is an example of one of the boards I did for a the guitarist from Plush/jacSharp and just wrapped up Ard Matthews from Just Jinjer's board as well (he was in such a rush I didn't get a chance to snap any pics).
You really want to use the least amount of cable as possible, the longer the runs, the more tone loss as the capacitance increases, the top end being the first to go.
RE buffers, yeah, having a whole bunch of buffered pedals do effect your tone, but buffers in many respects are a necessary evil, esp. if you have alot of pedals and alot of cable, they just help the signal along, so it is a catch 22, ideally you want to not have all your pedals buffered, but one or 2 are not bad, and best to have them at the front or end of the chain.
Your order seems pretty good, only thing for me is the need for the VS Route 66 and the Maxon, do you really need 2 TS's? The 66 is pretty much a part for part clone of a TS.
Cheers
Matt