I'll cover a couple things quick that are related.
a) The treadstone manifold doesn't have EGR ports. So what, block off the EGR valve. Install a 10,000ohm resistor at the EGR temp plug. No EGR codes. This also works if you have an EGR P0402
b) If you remove your cats or use non-oem cats, you will need a rear O2 simulator. You will still need to zip tie the O2 sensor out of the way, but with the rear O2 sim you won't have a cat efficiency code. You need to keep the O2 plugged in because the ECU monitors the O2 heater resistance. You can make a sim for about $15 or I can make and ship you one for $70.
OK, the URD Fuel and Timing controller is installed. This controller is $435 and works in-line with the OEM computer. It does a few things
1) Intercepts the OXY1 signal, modifies it, and sends it to the ECU. No matter what you do to change the fuel mixture, the ECU believes nothing is wrong and doesn't try to fight your changes
2) Intercepts the timing signal and modifies it. You can decrease timing anywhere.
3) Intercepts the MAF signal and modifies it. You can "richen and lean" out the mixture. The controller will also support up to around double the size of stock injectors.
Setup is pretty basic if you know how to cut, splice, solder, and tape. Directions are included along with an ECU pinout. Two of the colors are listed wrong for the ECU wires, but the location of the wires is correct.
The controller also has a vacuum hose coming out of it. The MAP sensor is built in and this is how it modifies the signal at various load points. Just tap into your boost gauge for the signal.
Without further delay.. pictures
Basic sensors running on Torque Pro
Logging with Torque Pro
Map "A" in the controller software (Fuel map) "10" is the ECU base value. You can go down to 0 (-2.5x) and up to 20 (2.5x fueling)
3D map of fuel map
Map "B" timing map "0" is the ECU base. By adding numbers to each load point you are actually reducing timing by that amount.
You can see the blue highlighted square. That square follows the map based on where you are real time.
3D map of timing map
Basic logging using the controller software. It records time, load, RPM and your values in Map A and B.
The only bad thing about all this is that you can't make real time changes. You have to make your adjustments, turn the engine off, write the file to the controller, and start the truck again. But I suppose you only really need to do this once and forget it. I'm just used to tuning with an AEM EMS where you can make constant real time changes of everything.
I'll be happy to help anyone get theirs setup, it's a little tricky to understand at first because there is a modified base map already installed in the controller when you first run it. You basically need to save this map to the desktop, create another one, and ensure the Map A is set to all "10s" and Map B is set to all "0's"