S3 2008 Won't Start

Yep, it is possible especially as it's only a 5A fuse.

 

I wouldn't think that a duff relay would blow the fuse as the coil circuit doesn't run off the 5a fuse . the relay is basically only connecting two contacts together so it either has a contact or it hasn't . You really need to disconnect the fuel pump and see if the fuse still blows as according to the wiring diagram the 5a fuse feeds a purple wire which realistically only supplies the fuel pump , immobilizer, and a 12v wire to the clocks . It could be a fault inside the immobilizer but I'm not sure if you can bypass the S4 datatool , I've done the S3 on a Daytona 600 and that was pretty easy

 

Basically ,as I've stated , the best thing to do to take the fuel pump out of the equation is to disconnect it and see if the fuse still blows . You could then run 12v direct to the pump , the purple wire is 12v+ , the black 12v- , that would tell you if the pump is functioning properly . FWIW I might be leading you in the complete wrong direction but not having the bike in front of me I can only give so much advice on a forum
Just been on you tube and it's piss easy to bypass the S4 alarm

 

As Paul Mac says confirm or eliminate the pump first, the 5A blowing fuse gives you a trail to follow. If the pump proves to be ok I'd look at the alarm next, you should be able to remove it from the system by reinstating the original jumper plug at the connector in place of the alarm, see my earlier post on another thread here.
Link to the plug is now out of date so try here or here

 

Should see a connector under the seat, follow cable from the alarm to the connector, unplug the alarm and put the looped plug in its place.

 

What else is on that fuse?

 

I would be checking those wires for breaks cuts nicks that short and blow the fuse.

 

One thing at a time.

 

Sooo o o ..... you HAVE checked the connector for bent/crossed pins, haven't you?