I have a troubleshooting idea for you......but PLEASE BE CAREFUL DOING THIS!
I would start by programming the unit for automatic transmission mode. You have to be really, really, careful though. You need to wait and think before you try anything. Check that the car is in neutral, parking brake on, and so forth. I would ONLY try the remote starter while seated in the driver's seat, so you can control it if it should suddenly move for whatever reason.
But anyway, put it in automatic mode and see if it will work. That way, you can troubleshoot your installation basics first---brake, hoodpin, toggle safety switch, and all that. You might have made a simple mistake in your installation that you just haven't caught yet.
Also, you know how to use the emergency key when the battery inside the FAST key fails, right?
OK, so suppose you put the Viper in automatic mode and it still doesn't work.
Next, put one FAST key far away from the car. Take the battery out of the other FAST key, and hold the gray square transponder part inside, close to the car's keyhole. Unplug your DBALL. Now try to remote start the car and see if it works.
The idea is to whittle the system down to its basics.....you can temporarily eliminate the manual-transmission stuff, and even temporarily eliminate the bypass module....... just try to get the remote starter itself to function. Then work your way back "up" adding one safety feature at a time until it fails....this way you know where to start troubleshooting.
P.S. You mentioned the plug-in toggle switch. It needs to be plugged in, and the switch moved to "On." If not, the remote starter portion won't work at all.
P.P.S. What are you using to make your diagrams? I really like them. I have a diagram I want to make, and I've downloaded TinyCAD (it's free) and I'm playing around with it a little bit.