Ran into a problem trying to fit back in my rear fender. All these wires are all tangled up and i don't know where they go. I'm sitting staring at the manual and it's hard to see what's what in the black and white pictures/diagrams. So if someone could pleaseee help me out and take a picture of the underseat assembly and if possible the wires that are under the ecu/battery. Here's the mess i have right now:

 

There is a small opening (box shape) if you lift that battery up that the battery goes into (just enough space for it). Once on there close the black lid and push down on the two thumb tacs (well buttons). From there you will that electrical unit on top (it's a proper fit and I believe can only fit one way). All that extra wires just gently place on the side if there is room

 

Yeah the wires are what's giving me problems. They are so short that they can barely move around and i think the starter relay and fuse box are supposed to clip onto somewhere?

 

I unhooked all of them and completely removed the entire fender for my undertail install this past week. Yes the battery goes in the battery box first. I beleive on my 03 that the negative terminal is on the right (exhaust) side of the bike. That should be evident from the black ground wire on the right side and the red positive terminal on the left side.

Put the battery in and go ahead and hook it up tightly. Watch out for metal on metal shorts when hooking up the terminals cause it's tight in there.

It doesn't look like you've unhooked anything so that should help. The starter relay is on the left sideand from you photos it doesn't look like you have moved it up so it should be out of the way. Looks like you really just need to get your battery back in the b-box first and then you'll have a lot more room. The ECM is easy enough to get back in place and don't be afraid to show it who's boss. The black plug side goes in the right of the bike with the flat part of the ECM on the bottom. I think the thinner part of the ECM faces the front of the bike to allow for the seat to fit. Sort of like an L shape if you are facing the right side of the bike.

It's not that big of a deal it just looks menacing if you have never done it before. Don't worry about that last little black plug that doesn't hook to anything as I think it's just a diagnostic port but I'm not sure.

 

Don't be afraid to unhook the plugs from the back of the ECM in order to test fit everything in it's place. I unhooked everything just to familiarize myself with each part. I also have a Clymer manual which helped.