I know I'm resurrecting an old thread but since this is the most informative thread about getting your turbo timer to work while having the factory alarm arm and doors lock while the turbo-timer is running I thought I would add this here.
in order to do the mod properly you will need the following in addition to all of the stuff for adding in the turbo timer.
2 automotive style relays
Extra wire: I used a good 10ft or more red (as you will be running it the length of the car), some blue, some yellow (didn't have orange wire for the alarm part) and some black.
Connectors: some of those tube wire connectors that you can use to connect wires together with, some spade connectors (if you don't want to do alot of soldering), a wire nut/twist connector, and one or two of the washer style connectors for grounding.
10 gauge size wire taps or whatever you used to install the turbo timer at the ignition source.
some electrical knowledge, patience, and the directions listed above.
Simply follow the directions about which wires to cut but install the relays inline with the wire instead of cutting them. For the blue and white wire that you cut at the wireless alarm wire you can add some wire into the line with the tube connectors and then connect to the relay (this is where the spade connectors come in, you will be using female). You can ground out the relay at the grounding point on the back deck where the size 10mm bolt is. then you run the Ignition switch power wire down the side of the car and up to the front of the car along the same path that your cars amplifier runs. You will be removing some of the cars trim such as the doorsill molding, but you can leave the stuff on the cab supports and just pust the wire up underneath it. Do the same for the orange pin 6 wire at your alarm. Run a ground and an Ignition switch power wire. I just tapped the ground into the ground for the turbo timer. connect both igniton power wires from the relay into a third piece of wire that you will use with the tap connector to tap into the igniton system wire. now this is where it gets tricky and you might need a voltmeter. THE WIRE YOU WILL BE TAPPING INTO IS NOT ONE OF THE ONES YOU USED FOR YOUR TURBO TIMER. this would cause it to not work properly. THERE IS A BLACK AND RED WIRE ON THE IGNITON SWITCH HARNESS THAT WILL ONLY SHOW POWER WHEN THE KEY IS IN THE ON POSITION. check it. turn your car on and let the turbo timer work, after you turn the car off you should notice that the power to this wire goes away. this is why it will work because it is not the wire that you used for the turbo timer. This wire is actually for the wiper system. CONNECT THIS WIRE TO YOUR IGNITION POWER WIRE THAT RUNS TO YOUR RELAY. now test, if it works then hide your wires and you will be good. also remember to insulate all the wires properly. if it doesn't work then you might have tapped the wrong wire or installed the turbo timer to your wiper power wire to begin with.
For the relays you will attach the wires to the following assuming you used the standard 4 lead SPST relay.
30: one side of the wire you cut be it blue/white or the orange pin 6 wire.
87: other side of the wire you cut be it blue/white or the orange pin 6 wire.
85: ground wire
86: ignition power wire
doing this will leave the wires connected when your key is in the on position and cut them with you have it in accessory, off or removed. This means that you can still arm the car while the turbo timer is running but not have to worry about the car arming itself or locking itself while you are driving down the road as has been reported by some people. this should also enable you to reprogram your cars remotes, and if it won't then you can just apply some voltage through the ignition power wire to turn the relays on and then program your key fobs.
hopefully this answers some future peoples questions about how to wire in the relays since I looked all over the forum and could not find a direct answer.