hah! I had the same problem with vacuum lines at first, but sorted it it out. Alas, mine's 5th gen, but you'll probably have to do the same process. I suggest you don't bother to tighten the boots until you make sure every hose can reach it's intended hole on the airbox.
First, I mis-aligned the hoses that go to the right-front to the left-front. Then I took the throttle body off and reset them to the correct place, but put the one that goes to the right rear up front. Then I realigned that and got them all together and had the grey connector going out the wrong side, but by then I had gotten smart and just let the throttlebody rest on the boots until I figured out what connected to what on the airbox and which hole it had to be routed through.
In the end, I figured it out through trial, error, and with a combination of both the manual AND the exploded diagrams from the parts fiche, which were much clearer showing hoses connecting to the airbox for some reason. Same with cooling hose routing.
When I put the thing back together the first time the fact that it turned over right away was a minor miracle. But, it did. And I've had the throttlebody off a couple of times since, due to that leak I told you about on the wax unit, and it started each time.
I wish you patience. That's going to be a cool bike when it's done - I love the RWB color schemes.
Keep us updated, too.