Build Info
Information on doing the modifications. This will be done 'blog style', where the newest information is posted on top.
Heat Exchanger
The 2.5" pulley on the supercharger has the ill effect of heating up the air charge and the SC itself considerably.
To combat this effect, 
a second heatexchanger was added in line with the stock one. TO achieve this, a Garrett HE was
mounted in the front grill, the outlet of the IC coolant pump pumping directly into it, and from the HE straight into the
aftercooler. From the after cooler, it runs through the stock HE and back to the pump (as it did stock). This modification significantly reduced the diference between IAT1 and IAT2 temps at WOT, and quickly cooled the charge back down to previous levels.
Timing Advance
Once the fuel was right where I wanted it, I could finally add as much timing as the engine would allow with out knocking.
The methods that I used to do this where a bit crude, but did the job. I raised the entire graph 1 degree at a time until I hit a bit of KR, and then backed it down one in only those cells. Rinse and repeat untill al the cells where at their maximum with out any KR. To be safe, after this process, I removed 1 degree of timing to account for any changes in fuel, temperature, or humidity.
Fuel tuning
Now that I had a good VE table to start from, I could log the PE AFR and make adjustments to the equivalence ratios to bring the AFR where I wanted. I picked a few key RPMs to watch, and adjust those accordingly to make them as flat as possible between 11.5:1 and 12:1.If the AFR was too rich I would VERY SLOWLY lower the equivalence ratio at that RPM untill the desired AFR was attained.
VE Table perfection
Tuning the VE to be really close to perfection took a lot of 
logging. It required me to disable the MAF sensor, add a little fuel by increasing the VE table by 10%, and then log commanded and actual AFR, at every RPM vs Air Mass I could. From these values, a table of 'AFR Error' can be generated, and applied to the VE table.
This creates a VE table that will run extremely close to the commanded AFR with out any other calculations from the MAF. From here I was able to recalibrate the MAF to be more accurate as well, as I now had a good reference. This made tuning the PE fuel a lot easier, as the graph is more linear than it would have previously been.
Wideband Install
Anyone who plans on tuning their car is required to have a wideband O2 sensor. I settled on the INNOVATE LC-1 because it sports 2 analog outputs, as well as a purely digital output for logging.
The analog outputs are fully programmable, so I decided to use one to emulate the stock O2 sensor, eliminating the need for adding a separate bung for the sensor.
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After wiring it up, I also decided to cut my rear O2 sensor cable, and program the LC-1 to output WB data to the ECM through that, so I could log it through HPTuners.
This set up took a little bit of adjusting (rear O2 setup that is) but was accomplished by comparing output of HPTunters, with that of the supplied LogWorks software. The install took very little time, and is a great solution for anybodies wideband needs.
Idle tune
Well, I was not going to attempt tuning my timing advance with out getting my fuel perfect. And I was not going to attempt
the fuel with out a wideband, so until that happened, I was going to tune drivability aspects, and get them perfect. I started with what haunts these cars with bigger injectors (and even a lot of stock cars, to a lesser degree). I needed to get this car
to idle, 
and not die at stop lights. AFter a little tinkering around, I found a solution. First, I played with the minimum injector pulse width, which kept it from dying all together. Then I created a short pulse adder table to smooth out
the flow when the pulse come close to nothing. This made it impossible for the car to die at idle, with out making it run rich. THe next problem was to find why the car was trying to overcorrect when hunting for the idle RPM. I decided to try
the idle over/under spin spark tables, and after about 15 minutes of playing with those, the car idled better than stock, while keeping the stock O2 sensor happy (sweeping from lean to rich around 14.7:1)
Pulley, Injector Install, and First Tune
The installation of the pulley had to wait until I had larger injectors in to accommodate the new high air flow. I was unable to
install new injectors with out tuning ability. Needless to say, all three of these things had to be put on in one sitting.
The first to go on was
the 2.5" supercharger pulley from INTENSE-Racing. 
To install this hardware, we thought it would be easiest to remove the blower,
and use a hydraulic press to get the stock pulley off. After greasing the SC shaft, we then used a power steering pulley installer to press the
pulley hub onto the shaft. The ring was then installed (NOTE: a 2.5" pulley requires machining of the supercharger snout!) with the 5 bolts provided, covered in LOCtite. The idler bracket was also removed, ground down to accept the larger idler pulley, and then reinstalled. After the blower was back on the manifold, the stage 2 belt was installed to ensure no slipping would occur.
To compliment this new found boost, the injectors had to be swapped for larger ones....90% larger ones. FIRST: I bled the the fuel rail from the schrader valve (ok, I actually didn't and ended up with a face full of fuel... but you should do this step to save yourself the embarrassment and dry face)
Then after removing the fuel rail, we uninstalled the stock injectors, and pulled out the stock harness. the new injectors were then placed in their stead, and the new wiring harness was installed to accommodate their Bosch style connector.
Before we put the newly equipped fuel rail in place, we cleaned out the injectors' seats, as they tend to accumulate dirt. After everything was reattached, it was time to update the stock PCM with a rough calibration to get the car running using HPTuners.
For starters, all I did was change the fuel flow curves, so the ECM would know how much fuel the new injectors would be flowing. These large injectors max out the chart in some areas, so editing of the VE table was needed to compensate. After removing a few things such as torque management, and any boost limits, I prayed quietly to myself, and turned the key.
It started right up! Stock O2 sensor sweeping and all, not too bad! My next account will be a little bit about the fine tuning of the system.
K&N Cold Air Intake
This intake was installed in mid June. The install was very easy and straight forward. We removed the front bumper to make it easier to get the stock intake parts out, and install the new intake system. The install took about 45min to complete. As I did this a while ago, I will post a link to instructions on how to do this modification.