Here is a link to a Pictorial on your 2006 Charger :   https://www.the12volt.com/installbay/forum_posts.asp?tid=132847
While the aftermarket equipment used is different, the wire colors and locations should be the same.
By "added the harness", I'm guessing you mean the DBI D2D harness as there appears to be no T-Harness available from 
XpressKit for your car.  ( I'm not a DB-ALL2 user...)  That would mean that the DB-ALL2 w/402.Chrysler Ver 5.06.01
firmware is connected to the Viper via the 4 Pin D2D harness and all the Blue dash lines in the Type 4 diagram are handled
by that harness.
The install is pretty simple with very few wire connections to the car.  Most of these connections are shown in the DB-ALL2
Type 4 diagram and photos can be found in the pictorial.  The only additional thing is the Viper siren wires.
Here is the wiring : 
Main Harness, 6-pin connector 
   H1/1       Red   (+) 12v Constant Input      to +12V Constant
   H1/2       Black  (-)   Chassis Ground     chassis ground
   H1/3       Brown  (+) Siren Output           siren
   H1/4       WHITE/ Brown    Parking Light  PIN 87a          not used
   H1/5      White Parking  Light Output   
*** Set to (+)   to WHITE/ Violet in PKP
   H1/6      Orange  (-) 500mA Ground when armed       not used
Door Lock 3-Pin Connector 
    (1.)      Blue        (-) 500mA Unlock Output        D2D
    (2.)      Empty   NOT Used 
    (3.)      Green     (-) 500mA Lock Output           D2D
H3 Remote start 10 pin heavy gauge harness 
     H3/1     Pink    (+)    Ignition-1 Input/Output        As per Type 4 diagram
     H3/2     RED / White (+)    Fused (30A) Ignition-2         not used
     H3/3     Orange       (+)    Accessory Output     not used
     H3/4     Violet          (+)    Starter Output ( Car Side )    As per Type 4 diagram
     H3/5     Green          (+)    Starter Input     ( Key Side )          not used
     H3/6     Red   (+)    Fused (30A) Ignition-1        to +12V constant
     H3/7     Pink/White (+)    Ignition-2 / Flex Relay Output         not used
     H3/8     Pink/Black   (+)    Flex Relay Input 87A          not used
     H3/9     RED / Black    (+)   Fused (30A) ACC/Starter Input     to +12V constant 
     H3/10    NC       No Connection 
Auxiliary/Shutdown/Trigger Harness, 24-pin connector 
(1.)      Pink/White       (-) 200mA Ignition 2/Flex relay Output    Not used
(2.)      Blue/White      (-) 200mA Trunk Release Output             D2D 
(4.)      BLACK / YELLOW    (-) 200mA Dome Light Output                 Not used
(5.)      Dark Blue        (-) 200mA Status Output               Not used
(6.)      WHITE/ Black     (-) 200mA Aux 3 Output                Not used
(7.)      WHITE/ Violet     (-) 200mA Aux 1 Output                Not used
(8.)      ORANGE / Black   (-) 200mA Aux 4 Output               Not used
(9.)       Gray (-) Hood Pin Input (NC or NO)             to kit supplied hood pin switch
(10.)     Blue   (-) Trunk Pin/Instant Trigger Input              D2D
(11.)     WHITE/ Blue   Activation Input                       Not used
(12.)     Violet/White*        Tachometer Input          D2D
(13.)     BLACK/ White** (-) Neutral Safety Switch/Parking Brake input      D2D  ** Could go to Chassis Ground
(14.)     GREEN/ Black     (-) 200mA Factory Alarm Disarm Output    D2D
(15.)     Green*    (-) Door Input           D2D
(16.)     BROWN / Black    (-) 200mA Horn Honk Output        Not used
(17.)     Pink   (-) 200mA Ignition1 Output              Not used
(18.)     Violet*   (+) Door Input          Not used
(19.)     Violet/Black     (-)   200mA Aux 2 Output              Not used
(20.)     Brown   (+) Brake Shut down Input            D2D
(21.)     Violet / YELLOW    (-) 200mA Starter Output              Not used
(22.)     Gray/black       (-) Diesel Wait to start        Not used
(23.)     Orange    (-) 200mA Accessory Output         Not used
(24.)     GREEN / WHITE    (-) 200mA Factory Alarm Arm Output      D2D
While I am not a Viper user, I believe you can combine the three necessary +12V constant input wires into one and fuse
this one connection down to 20 - 25 amps.  The +12V constant wire shown in the Pictorial should be suitable for this but
you could always go directly to the battery, too.
Question #1... The H3/7-pink/white wire Ignition-2 / Flex Relay Output, What does it mean? The car wiring data info says same as ignition-1 ? Do i wire up a connection using a relay which i do have, if so please guide me, i just need a boost toget started.. 
Answer #1 :  H3/7 is not used/needed for your application.  
Question #2.. Does the H3/8 Pink/Black wire go with a mentioned above relay but goes in 87a ? Diagrams please share or which should i follow.. 
Answer #2 :  H3/8 is not used/needed for your application.
Question #3... Does the 5906v have already a kill switch built into it,. I am confused with H3/4 Violet (+) Starter Output( Car Side of Starter Kill ) AND H3/5 Green (+) Starter Input     ( Key Side of Starter Kill )... If it don't do i wire up a kill switch wiring? Which Kill switch diagram should i follow? 
Answer #3 :  Slightly longer answer.  The Charger may or may not have a Factory alarm system.  The Viper is an alarm
system and monitors the doors, trunk and hood.  So, do you need/want additional security?  The "Starter Kill" relay is built in 
to the Viper.  No need to add an external relay.  Wired up as shown above and in the DB-ALL2 Type 4 diagram will work 
fine but not use the Vipers Starter Kill and Anti-Grind functions.  You could try it this way first, make sure everything works
OK before cutting the cars Starter wire and adding in the Vipers thick Green wire.
Question #4... H3/3 Orange (+) Accessory Output,, Do i connect this wire to a ACC wire in vehicle? 
Answer #4 :  Your car does not have an actual Accessory wire and does not need either the Vipers thick (+) Orange
Accessory wire or the thin (-) Orange Accessory wire connected.
Soldering is fun!