Viper 4806v MTS mode

Hi All,
First off:
-I am not a professional installer
-I am an electrical engineer, with understanding of complex electrical systems
-I only have the quick install guide for the 4806v, and an install guide for a similar system

With that out of the way, I am installing the system into a 1998 4runner with manual transmission. I have successfully installed the unit into the vehicle only connecting the wires that I felt were needed to make the remote start work (I'm planning to connect the rest up later - a minimal install).

When I program the unit into Automatic mode (just as a test - don't worry guys - I didn't leave it) it worked fine. The car started and everything was good and happy. I also tested to make sure the tach was configured correctly by attempting to start the vehicle with out the connection - it failed as expected so I know that the tach is configured and correctly connected.

Then I programmed the vehicle into manual transmission mode and attempted to enter the reservation mode (in order to remote start the vehicle). This is where the failure occurred. I started the vehicle with the key, then pressed the foot brake, pulled the hand brake, released the foot brake then pressed the remote start button on the FOB. The FOB then played a sound that I can only describe as "I can't do what you asked me to" then when I removed the key to begin the exit procedure the engine turns off instead of remaining to run (and wait for me to exit the vehicle and press the lock button)

I have connected the following signals:
Main Harness, 6 pin connector
H/1 RED    (+)12VDC CONSTANT INPUT
H/2 BLACK (-) CHASSIS GROUND
H/3 BROWN (-) 200mA HORN HONK OUTPUT
H/6 ORANGE 500 mA GROUND WHEN ARMED OUTPUT
did not connect pin 4 & 5:
H/4 WHITE/ BROWN LIGHT FLASH ISOLATION WIRE - PIN 87a light flash relay
H/5 WHITE PIN 30 of LIGHT FLASH RELAY

Remote Start, 8-pin connector
1 RED / BLACK (+) 12VDC CONSTANT INPUT for ACC and starter relays
3 PINK/WHITE (+) IGNITION 2 / FLEX RELAY OUTPUT
4 RED        (+) 12VDC CONSTANT INPUT for ignition 1 relay
5 VIOLET     (+) STARTER OUTPUT
6 ORANGE     (+) ACCESSORY OUTPUT
7 RED / WHITE (+) 12VDC CONSTANT INPUT for ignition 2 and flex relays
8 PINK       (+) IGNITION 1 INPUT/OUTPUT
did not connect pin 2:
(+) FLEX RELAY INPUT 87A key side (if required) of FLEX RELAY

*did not connect door lock connector
*did connect neutral safety switch
*did connect control center

Auxiliary/Shutdown Harness 24-pin connector:
9 GRAY (-) HOOD PIN INPUT (NC OR NO)
12 VIOLET/WHITE** TACHOMETER INPUT
13 BLACK/ WHITE*** (-) NEUTRAL SAFETY /PARKING BRAKE INPUT
15 GREEN** (-) DOOR INPUT
20 BROWN (+) BRAKE SHUTDOWN INPUT

A question:
there is
15 GREEN** (-) DOOR INPUT
and
18 VIOLET** (+) DOOR INPUT
These wires perform the same function so only one of the wires is needed, correct? I only used the (-) input because that's what the vehicle uses...

Any and all input and suggestions would be very much appreciated. I have spent a lot of time being very frustrated >:(

Thanks!

Do you have all doors closed when trying manual transmission mode?
Is there any bybass module being used?
Did you do the tach learning procedure?

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Strange that it worked OK when in Auto Trans Mode without the Neutral Safety Switch plugged in and set to ON.  Think I would double check the (-) Door Trigger Input and the (-) E-Brake Input ( to NSS ).

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Soldering is fun!

Sorry, I did connect the neutral safety switch and it is in the on position.

I did have all doors closed. I should try group ding the door input. It won't let me remote start the vehicle because it won't detect the doors opening, but it should let me enter I to reservation mode, yes?

There s no bypass module.
I should also mention that pin 6 was not connected either.

I will loom a little further into the door and ebrake and see what happens. In the mean time, any further comments are welcome :)

Oh, and I did do the tach learning process when I started it in automatic mode. But the tach is a hardware tach and set as such in the menu system so I dont believe there is a learning process?

There is a learning process for tach. After you start the vehicle with the key you have to press and hold the valet button within 5 seconds. When the LED lights up release the button and tach has been learned. Even though the brain is set for it it still has to be learned.