Mopar keyless entry on '98 Dodge Ram 1500

I wanted to program a new remote transmitter for my newly purchased truck.  I found one and tried to follow the instructions but the switch under the dash, to place the unit in programming mode, was not working.  Further investigation revealed a bunch of 4 wires, as a unit, pushed out the back of the switch body!   Two seemed to be connected to an LED (?), the other two to bare terminals.  

After this, I found the original remote was not working.  Called the helpline at Mopar, they said take it to a dealer (potential charge $21!)

The dealer says the module is U/S and the cost for a new one is $318!  Fortunately they didn't charge the $21.   I said forget it!   Later, on inspection, I found the switch body no longer existed and the wires are just tucked under the dash.  I also found a blown 20A fuse in a pink wire to the module.   I replaced this and did some research online which suggested just connecting the two bare terminals as the switch could only have done that. 

I tried this but still nothing.  I've tried to take out the module, but then the power door locks don't work, so I need to maintain the wiring continuity by leaving the module in circuit.

My questions....

Firstly...what is the grey sheathed wire that comes out the back of the module and disappears up behind the dash?  I don't fancy trying to get up behind there!

Secondly, I have a large connector and a smaller one into the module, located down by the brake pedal.  How can I best work out what connects to what to remove the module and keep the power door locks working?

Thirdly,  Can I use these wires to hook up a new keyless entry system from Commando Alarms without having to break into any other wires?  Obviously I can't use the existing connectors, but maybe the wires?   Whats the best way to connect two wire ends?

Sorry if there's alot of questions, but I'm a mechanical design engineer with a basic understanding of electrics, and black boxes are literally that to me..black boxes!   But I can work it out with some knowledgeable advisors!