SOURCE: battery went dead,clifford alarm locked the engine
Assuming that all is well with the vehicle's electrical system (fuses, etc...), the following should work, as Viper/Clifford uses the "fail safe" method of starter disable, and it only works to lock out the starter when the alarm is functioning properly and in the armed state.
That system has a "starter kill" system. When the alarm is actived, the starter kill is engages, and won't let the starter get voltage from the ignition switch. First thing I'd try is connecting the car's battery while the ignition key is turned to the "on/run" position. Cycle the alarm to arm, then disarm, so that the LED is not blinking. It also may require using the manual override button/switch (with the key on) to reset the alarm. Should start after that.
If all else fails, reconnecting the starter wires back together (they are spliced and running through the alarm via a SPDT relay.
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