I would split the Viper input power between the two +12V constant wires on the Jeep. That will not cure your current issue, but will be better for current balancing once you get it working.
No, the Viper 4105 shouldn't need to be flashed before use. It should work right out of the box. There might be some programming changes that need to be made at some point.
Something like this should work :
Viper 4105 to 2001 Jeep Cherokee
Main 9 Pin
1 LIGHT GREEN/BLACK FACTORY ALARM DISARM
2 GREEN/WHITE FACTORY REARM
3 YELLOW (+) IGNITION OUT (TO ALARM) not used
4 WHITE/BLUE (-) ACTIVATION INPUT not used
5 ORANGE (-) GROUND WHEN LOCKED not used
6 BROWN (-) HORN OUTPUT BLACK/RED (-) @ STEERING COLUMN HARNESS
7 RED/WHITE (-) TRUNK RELEASE OUTPUT not used
8 BLACK GROUND chassis ground
9 WHITE (+/-) LIGHT FLASH* set to (+) BLACK/YELLOW (+) @ HEADLIGHT SWITCH
R/S 5 Pin
1 BLACK/WHITE (-) NEUTRAL SAFETY SWITCH INPUT Chassis Ground
2 VIOLET/WHITE TACHOMETER INPUT WIRE GRAY @ PCM, BLACK Plug
3 BROWN (+) BRAKE SWITCH SHUTDOWN WIRE WHITE/TAN (+) @ SWITCH ABOVE BRAKE PEDAL
4 GRAY (-) HOOD PINSWITCH SHUTDOWN WIRE kit supplied hood pin
5 BLUE/WHITE (-) 200mA 2ND STATUS/REAR DEFOG not used
4-pin satellite harness diagram
1 BLUE STATUS OUTPUT not used
2 ORANGE (-) ACCESSORY OUTPUT not used
3 PURPLE (-) STARTER OUTPUT not used
4 PINK (-) IGNITION OUTPUT not used
Heavy gauge 6 Pin
1 RED (+) (30A) HIGH CURRENT 12V INPUT RED (+) @ IGNITION SWITCH HARNESS
2 PINK/WHITE (+) PROGRAMMed to IGN BLACK/ORANGE (+) @ IGNITION SWITCH HARNESS
3 RED (+) (30A) HIGH CURRENT 12 INPUTPINK/BLACK (+) @ IGNITION SWITCH HARNESS
4 ORANGE (+) (30 AMP) OUTPUT TO ACC CIRCUIT BLACK/WHITE (+) @ IGNITION SWITCH HARNESS
5 PURPLE (+) (30 AMP) OUTPUT TO STARTER CIRCUIT YELLOW (+) @ IGNITION SWITCH HARNESS
6 PINK (+) (30 AMP) OUTPUT TO IGNITION CIRCUIT DARK BLUE (+) @ IGNITION SWITCH HARNESS
Door lock harness, 3-pin connector
1 BLUE (-) UNLOCK OUTPUT PINK/PURPLE (TYPE B) IN DRIVERS KICK PANEL
2 EMPTY NOT USED
3 GREEN (-) LOCK OUTPUT ORANGE/PURPLE (TYPE B) IN DRIVERS KICK PANEL
Soldering is fun!