So I just spent the past five hours working on the bike.. time really flies when you're doing menial tasks like soldering. Here's how the controller fits inside the frame:

I had to reconstruct the batteries to 3s blocks instead of 4s because 4s wouldn't fit inside the frame. This is a very annoying task. And I also have to build a printer cable port so that I can balance charge my packs if needed, that's a lot of work still needing to be done. Can anyone suggest a printer cable thing that has at least 17 pins? Not too many either, I'd like it to fit in the little space left in the frame.
All I did after taking a break from battery work was wire up the throttle, CA, and misc switches like cruise and three speed.
Here's the issue I'm having though.. wiring it all up, I get one of two problems. One is that the throttle doesn't work, the other is that right when I turn it on I already get full throttle. I can't seem to work out the combination for the throttle and since I have the same throttle and controller as my last build, I wish I could look but that one is sealed up also. Will have to work on it again tomorrow.
Edit: throttle issue worked out.. bike is up and ready to go, just have to finish the battery setup. I got my hands on a SATA plug so will have to wait for that to come in to build a balance port.