viper 5704 scion xb

So I've installed viper 5704 alarm on my wife's 06 xB 5speed over the weekend but i'm having some problems with it. Also added glass break sensor and tilt sensor, just haven't tested them yet. The only functions right now is door/lock unlock and shock alarm. Cant get remote start to work, getting an error message on my remote and headlight flash 7 times which means manual transmission mode is off. Cant enable MT mode with remote, tried a few times. Also can't pair my remote with the brain, tried from remote function menu and using control button on the antenna. I don't understand how I'm able to use remote to lock/unlock and read messages, but its not paired? Tried to disconnect the battery for 30min,still doesn work. Here is my wiring, let me know if i missed anything. Thanks

Main Harness

h1/1 red const 12v - tap to a const 12v WHITE/ red - ignition harness
h1/2 black grnd - chassis ground
h1/3 brown siren out - connect to sirens red (black to ground)
h1/4 WHITE/ brown park light isolation wire - not used
h1/5 white park light out - tap to park lights green wire - headlight switch
h1/6 orange ground when armed out - not used

Door lock

1 blue out - tap to neg unlock -yellow/black -driver kick
2 empty
3 green - tap to neg lock-blue/white -driver kick

Aux/shutdown/trigger harness, 24-pin connector

h2/1 pink/white ign/flex relay out - not used
h2/2 BLACK/ white neutral safety input - tap to e brake -black
h2/3 blue white 2nd stat/rear defog out - not used
h2/4 green black oem alarm disarm out - not used
h2/5 RED / white trunk release out - not used
h2/6 green door trigger in - tap to door trigger RED / white - fuse box 9pin

h2/7 BLACK / YELLOW dome light supv out - same as door trigger

h2/8 BROWN / black horn honk - tap to horn WHITE/ red-steering column
h2/9 dark/blue status out - tap to clutch switch-BLACK / YELLOW
h2/10 pink ign out - not used

h2/11 WHITE/ black aux3 out - not used
h2/12 violet door trigger in - not used
h2/13 WHITE/ violet aux1 out - not used
h2/14 violet/black aux2 out - not used
h2/15 ORANGE / black aux4 out - not used
h2/16 brown brake shutdown in - tap to brake wire switch green red-brake pedal

h2/17 grey hood pin - to hood pin
h2/18 violet yellow starter out - not used

h2/19 blue instant trigger in - not used

h2/20 grey/black diesel wait to start - not used
h2/21 WHITE/ blue remote start/tt acvt in - not used
h2/22 orange acc out - not used
h2/23 violet/white tach in - tap to tach black wire- obdII connector
h2/24 oem alarm out - not used

remote start 10 pin heavy gauge connector

h3/1 pink ign in/out - tap to ignition black - ignition harness
h3/2 RED / white fused ign2/flex relay in - not used
h3/3 orange accessory out - tap acc blue/red - ignition harness
h3/4 violet start out - cut black starter wire then connect this to starter side

h3/5 green starter in - key side of cut starter wire

h3/6 red ign in - tap to const 12v WHITE/ blue-ignition harness
h3/7 pink/white ign2 out - second ignition BLACK / YELLOW-ignition harness
h3/8 pink/black flex relay in - not used
h3/9 RED / black acc/starter in - tap to const 12v WHITE/ blue-ignition harness

H3/2 RED / White goes to +12V constant WHITE/ Blue, also.  It powers the Flex Relay Pink/White output for Ign2.

Verify the two Black wires at the ignition harness with a DMM.  One is Starter and the other is Ignition1.

Is the Neutral Safety Switch plugged in and set to ON?

Did you verify the Door Trigger wire with a DMM?  Some conflicting info on
it.  DEI says it is Red, while Bulldog and Audiovox say it's RED / White.  Here
is Omega's info :
Dome Light         RED (DR),RED / WHITE(PS)         13 PIN CONN ON BACK OF FUSE BOX *

This would come into play with Viper programming and MTS mode setup/entry.

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Soldering is fun!

Thanks, i'll try to solder H3/2 to WHITE/ blue tonight. I verified black ignition and starter wires with tester, before cutting starter wire. Switch is plugged in and on, but i'll check it one more time, maybe it came loose. Too bad i put the brain so far up in the dash, its almost impossible to check any connectors without removing the whole dash. I'm pretty sure door trigger is good, because if i try to arm it with the doors open, my remote says the door is open. I tapped both H2/6 and H2/7 to RED / white, top of the fuse box, 9pin plug.

Alright, got it to work finally. Thanks! I can remote start it but still have to hold clutch in. H2/9 dark/blue status out is hooked up to BLACK / YELLOW at clutch switch. Is that right? Also how to i get little shifter icon to show up on my remote screen?

Info on bypassing the clutch pedal interlock is difficult to find. 
Does you xB have cruise control?  If so there are 2 clutch pedal
sensors, one for the cruise disengage and the other for the starter
circuit.  It's usually a matter of testing with a DMM to figure out
which is which and then using the DMM to figure out exactly what the
switch does.  Typically, it is a circuit that is open until the clutch
pedal is depressed almost to the floor.  Whether it passes a ground or
a +12V signal at that point depends on the vehicle.  There is usually
an input wire and a output wire.  If your system uses a ground signal
and the output wire is BLACK / YELLOW, you should be OK.  A more common
way to bypass this clutch switch is to use a relay wired as below :

Relay Pin 85 to R/S (-) Starter Output ( or GWR )
Relay Pin 86 to +12V constant thru 3 Amp fuse
Relay Pin 30 to one side of the clutch pedal Starter interrupt switch
Relay Pin 87 to the other side of the clutch pedal Starter interrupt switch
Relay Pin 87A - not used - insulate

Wired like that the actual polarity ( + or - ) of the wire does not matter.
Neither does which wire is input or output and any signal current demands
are met/handled by the relay.

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Soldering is fun!

The Manual Transmission shift lever should show up on the LCD display once you have successfully enabled / entered
into "reservation" mode.

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Soldering is fun!

Now I see what I did wrong here. It would work but unfortunately xB CIS does not use ground system. Black wire has 12v at the startup. I will pick up a relay and some fuses tonight. Hope I didn't mess anything up in there because I had H2/9 ground going to 12v the whole time I remote start the car. I was wondering if I can use alarm inputs/outputs to power up my relay? H2/18 to 85, H2/9 to 86 and CIS wires in parallel to 30 and 87? Are those 200mA inputs/outputs enough to power up relay or not?

H2/18 and H2/9 are both (-) signals.  It won't actuate the relays' coil.  Pin 85 should be (-) and Pin 86 should be (+).  You can also use H2/3 as another (-) GWR Status Out signal for Pin 85.

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Soldering is fun!

Relay worked like a charm for clutch bypass. Thank you. Now the new problem is i can't get it to work in mts mode when i get out and arm the car the engine will stop. My car stays in pit mode for some reason, just keep running. Do you think its door trigger/ related problem? Door trigger works fine to me, and dome lights i don't even have a light bulb in there right now and i always keep it at off position. idk

First, verify that you are set for Tach mode, Menu 3, Item 2, Option 4.
Tach Mode is mandatory for a Manual Transmission install.  I believe the
newer Vipers will automatically switch over to Tach Mode if you do a
successful Tach Learn but forcing it via programming and then performing
the Tach Learn procedure can't hurt. 

Second, I don't believe Dome Light Supervision is necessary on your
vehicle.  Does the dome light come on when you use the Factory Remote
to Unlock the car?  If it does, you don't need that connection from
the Viper.  Delete that connection and see if the symptons change.

It is usually best to use the actual Door Pin Switch as the input.
Using the Dome Light can cause problems due do any factory delay or
fade-out built into the vehicle.  If you can locate the actual individual
door pin wires, combine all the door pin inputs ( isolating with 1N4004
diodes ) on to the Viper's Door Trigger input.  No one lists those wires.

Info from DEI :
Door Trigger       Red (-)          top of fuse box, white 9 pin plug, pin 1

Info from Bulldog :
DOOR TRIGGER     RED / WHITE ( - )     @ TOP OF THE FUSE BOX, 9-PIN PLUG

Info from Audiovox :
All Door Trigger    RED / WHITE  (-)  IN PLUG AT VEHICLE FUSEBOX

If the RED / White wire at the 9 Pin Plug at the top of the fuse box is an
actual "All Door Trigger", it should work for the Viper alarm function,
Viper programming function and entering into MTS reservation mode.  Test
this wire with a DMM using all doors to verify.

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Soldering is fun!

Do you know where I can find good viper manual with all the programming menus you are talking about? I looked in the book it came with and 5704 guide on viper website but I cant find anything about menus in there. Thanks.

DEI Viper provides those install manuals to authorized dealers only.  That being said, you will
find some Viper manuals in the downloads section.  Unfortunately there isn't one posted for
you new style 5704 system.  You should be able to glean enough info by referring to the
5704 guide ( https://www.the12volt.com/installbay/file.asp?ID=1126 ) and the 5904 guide
( https://www.the12volt.com/installbay/file.asp?ID=1112 ).  The programming tables should be
the same.  While the connectors have been consolidated on the newer unit, the wire name,
color and function should be the same.  The older ( 5901 ) guides sometimes give better
explanations for wires and programming functions, so don't be afraid to really dig in for some
exciting reading. 

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Soldering is fun!

Soon as i programmed the tach everything started to work just how i wanted MTS mode makes me feel pretty safe now. Thanks for the guide kreg357, i had no idea all those options could be programmed. I really appreciate your help, you sure know your stuff.