Sounds like it could be a temp sensor to me?

 

Your alarm more than likely didn't cause the problem you describe. On my '03, my remote wasn't very responsive, even with a new battery. Keep trying to disarm the alarm with the remote. If I remember right, you hold the button in for a few seconds to arm it and click twice to disarm (or something like that).

 

You need to click twice (like a computer mouse) to disarm the alarm. I agree with the temp sensor or ignition problem

 

I think the temp sensor problem is possible here. Though i don't have any wiring diagrams, so if you could just tell me where is it possibly located so i could check on that, i'd be very grateful.

 

Behind the horn - this from page 4-20 2008 Touring Service: Fuel System

ENGINE TEMPERATURE SENSOR (ET)

REMOVAL
1. Remove maxi-fuse. See 8.5 SYSTEM FUSES AND RELAYS.

2. Loosen horn bracket bolt to front cylinder head. Remove horn bracket bolt (with flat washer) from rear cylinder head and swing horn bracket forward.

3. Pull back boot at back of front cylinder and remove ET sensor connector [90].

4. Slide a deepwell socket over the sensor body hex and turn counter-clockwise to loosen. When sensor turns easily, pull out the deepwell socket and remove sensor by hand. See Figure 4-25.

 

I had a similar symptom on my '00. I had a fuel management system on it that developed a problem - basically, it just went nuts. Once I removed the system from the bike it ran great. However, my non-start issue was very intermittent.

I agree with a few folks about your bike - check the temp sensor.