This is a pretty confusing situation with apparently more than one electrical fault.
The indicator wire short that caused the Accessories fuse to blow has been sorted but that appears to be a parallel issue that shouldn't have stopped the starter from cranking.
Going right back to the original issue it sounds like the engine stopping might not have been fuel because reserve would normally take you further than 20km (approx 12 miles). However, first things first - to get the starter to crank.
You have checked the fuses and the relays with a multimeter (you can check the coil and the NC (normally closed) contacts of a relay with a multimeter but you need to energise the relay to actually check the NO (normally open contacts).
Refer to page 7-16 in the Firebolt Service manual that is downloadable on this site for the procedure).
The starter relay has power supplied to its coil via the handlebar start switch. You can check to ensure the relay is getting power and ground by measuring at the relay socket. I have taken a photo of the relays for my '06 Uly with the Start relay removed and the Power and Ground connections labelled.
If you remove your Start relay (ignition switched off) and measure for DC volts in the power socket - the meter probes are probably too wide to fit so use a piece of bared wire attached to the probe). You should see +12volts DC with respect to ground if you have the ignition switched ON, kill switch ON and starter button depressed.
For the Start relay to operate you also need a ground return. The Start relay ground includes the clutch and neutral switch interlock. This interlock has a diode that isolates the clutch switch from the Neutral light (it is the black item in the far left of the photo) so you will be measuring a diode if you try to measure resistance from the ground lug shown on the relay to a ground point.
If your multimeter has a Diode range (one position should have that symbol shown on the black diode above), with the red meter lead on the relay ground point and the black lead on a ground point you should measure the voltage dropped across the diode junction (0.65v on my meter).
If you put the multimeter on the resistance range and measure from the ground lug of the relay to a ground point (ignition off) you should measure an open circuit - pull the clutch in and this will drop to zero (assuming good connections) or something like 1 or 2 ohms.
If all these checks indicate the relay should be working then you can do the next test (carefully). The two vertical lugs in the relay socket (to the right in the picture above) are where the high current NO contacts are connected so with the relay removed, Ignition ON, and kill switch ON jumping these contacts should result in the starter cranking - just a momentary jumping should result in a load click from the starter solenoid and be enough indciate the state of play.