So here's the problem... you just confirmed it before lazyxj had a chance to get back to me on his switch. The original idea was to make it so that the timer was triggered when the ignition was shut off. Setting Jumper 4 to A told the timer to start when (ignition switched) voltage was removed from the trigger. The problem is, regardless of the setting of Jumper 4, the built in relay was being activated (thus turning on the fan) as soon as the trigger wire received power from the ignition. As I mentioned earlier in the thread, the info provided by ELK wasn't very clear on whether the trigger activated just the timer, or both the relay and timer.
What is happening is that when you turn on the ignition, the relay is being activated by the application of 12V+ at the trigger terminal. It stays on because Mode A is waiting for this voltage to disappear before starting the timer. As soon as the ignition is turned off, the timer is triggered and the built-in relay shuts off when the countdown is over.
The easy solution is to attach the trigger wire to a momentary switched 12V+ source. When you want the fan to run a timed cycle, you hit the momentary switch and the fan runs for however long you set the timer for. (You just proved this works when you were tapping the trigger terminal with the trigger wire.) The only problem with this is that the fan does not turn on automatically as was originally desired.
I guess the next question is how badly do you want it to run automatically? It would involve including another relay in the circuit. It could be placed right next to the timer as all the necessary wires would be available there. I'm at work so I can't draw it out right now, but here's how it would go:
"Plan C"
The current trigger wire would be disconnected from the timer and re-connected to terminal 86 on this additional relay.
Terminal 85 would be connected to ground.
Terminal 30 would be connected to your constant 12V+ source.
Terminal 87a (N/C) would be connected to the trigger terminal on the timer.
Trigger Mode (Jumper 4) would be switched to Mode B.
Here's how it would work:
When you turn your ignition on, this additional relay would take power away from the trigger terminal on the timer. This would prevent the built-in relay from turning on. The fan would run only when the PCM told it to.
When you turn the ignition off, this additional relay would apply power to the trigger terminal. With J4 set to B, this application of power would trigger the relay to turn on and start the timer. The timer would do it's countdown and shut off the built-in relay when it hit zero. The trigger would still have 12V+ on it, but the timer would prevent the relay from staying on.
There may be a cleaner way, but if there is I can't think of it right now. I don't particularly like the complexity of having 3 relays in the system, but it's the only way I can see it working automatically.