viper 5301 on 2003 ford f150

Need symptoms, like no crank or cranks but won't start.  Which wire actually shorted?   Here are a couple of things to check.

Did you install the "Starter Kill" relay & cut the trucks starter wire?   All connections should be soldered and insulated, espically these.

Is the "Key in the Box" bypass on all the time?  Unplug the power to the bypass and try a ignition key start.