trying to bypass alarm system

Hello, I'm attempting to diagnose a 1999 chevy astro van that won't start. I've eliminated all of the easiest to determine culprits and I need to make sure that the alarm isn't somehow in a mode that's disabling the ignition before I go any further. The car was purchased used with an installed Viper 771xv. Because the battery had also died before I started diagnosing, I have no idea what the restoring/default behavior of the alarm system is. I've taken a detailed look through the installation manual and performed what they call shut down diagnostics using the valet button and the led flashes six times which corresponds to '(-) Shutdown (h3/3 gray) or (+) Shutdown (h3/4 brown)' I've got virtually no experience with alarm systems, but am generally knowledgeable with car electronics. I don't know if this procedure is doing what I want (to temporarily disable every alarm component) ? Before diagnosing the car would turn over just fine, after performing the 'shutdown diagnosis' attempting to start the car simply causes a rapid clicking from the starter region. Unfortunately the car is miles away at a friends house without internet access so I'd like to go back there with as much information as possible. Thanks for the help in advance!

Have you checked the battery and the connections at the battery?  If so, look under the dash near the steering column, there should be a yellow wire that was cut and then both ends were ran to a relay.  Remove the relay and reconnect the yellow wire back to itself.  This will remove the starter kill portion of the alarm. 

Thanks! I have previously checked all the battery and connections. Could the wire you're referring to be perhaps red? Of the heavy gauge wires going into the relay box, none are yellow. here's a schematic of the relay box.

Yellow wire on the vehicle, purple hooked to one side of it, and green hooked to the other side.A DMM is a beautiful thing.

MECP Advanced Installer Certified.