[Crackshot]

So how do you know it's in neutral?
The light is working? No dimming of the lights that says the headlight is coming on? (just need to be sure)

There are 4 connections on the starter relay (mis named the solenoid).
The signal (low current 12 volts, thin wire)
Ground (low current ground, thin wire)
Power in (high current 12 volts, right from the battery, large wire)
Power out (Directly to the starter, large wire)
The relay is (I believe) on the right side of the bike. Is it clicking?
If you jumper the large wires on the relay (with large wire or tool) will the starter spin (this will create arching so be careful, you can weld the wire to the post or damage the post)? Can you see 12 volts on the thin wires when you press the starter button? No 12 volts on the thin wires means a bad connection somewhere or an interlock not made. You need the right wiring diagram to trace out where the signal is being lost.
The actual wiring of the bike is probably the same from 88-06 but the colors might be different and it can be a bear following the signal without having the right color codes..

Awesome, this is a lot of good information.

I know it is in neutral because the neutral light is on and the back tire moves freely.

Also an update, I cleaned the connection to the tank and the gas gauge now works properly.
I am going to work with the voltmeter when I get home.

And yes, the headlight is on and working properly.
To surmize: Everything electrical is working perfectly except the ignition process.

[Black_peter]

And yes, the headlight is on and working properly.
To surmize: Everything electrical is working perfectly except the ignition process.

OK, just didn't want to take anything for granted..
Do you have the wiring diagram? I seem to remember that someone posted the 98+ diagram here..

I can work up a test path if you want.

[Crackshot]

OK, just didn't want to take anything for granted..
Do you have the wiring diagram? I seem to remember that someone posted the 98+ diagram here..

I can work up a test path if you want.

No, I don't have a diagram, which is why I'm having so much trouble. I'm having to try to figure this out via trial and error. At least this time I worked on it I have a garage, lol.

I suppose the biggest problem is identifying the parts you are talking about. I'm not a fan of bypassing relays I can't Identify perfectly, lol.

Do you have any thoughts on that pic I posted?

[Black_peter]

Do you have any thoughts on that pic I posted?

None what so ever.
I don't know 98+ well enough..

[steves]

The picture you posted is too blurry/washed out for me to read the color of the wires off that plug.

http://katriders.com/vb/showthread.php?t=56167

[Crackshot]

The picture you posted is too blurry/washed out for me to read the color of the wires off that plug.

http://katriders.com/vb/showthread.php?t=56167

Gah sorry. Thanks for the link!

And the circled cable is black, the one below it is white/yellow and black

I'm pretty sure this matches my picture perfectly. And if that wire is broken, it seems fairly safe to say that it would effect my starter.

[brooder]

This is going to sound odd, but did you try putting it in gear and hold in the clutch to start? I had this same issue on my 02 when I first bought it. It would not start without the clutch in, in gear or not. Neutral with no clutch and it would stare at me like a deer in headlights. Turned out that the PO had bypassed the sidestand switch. Hearing the phrase "bypassed switch" always makes me think it's that switch.

Also, download the service manual. It has the 98+ wiring diagram in it.

[Crackshot]

Well, the clutch switch has been completely bypassed. (literally there is a wire connecting both leads of the switch) so I'm pretty sure that isn't the problem.