To bring this thread up to date, I've been slowly finishing up the final touches.
The clutch master cylinder is now bled enough that I'm happy with it.
I tightened up the exhaust to get rid of my leak @ the y-pipe, and things sound much better now.
The boost gauge is installed, and the wideband o2 gauge is about halfway installed. (Had to customize the gauge pod more than I expected) I'll finish that up the next chance I have to work on the truck.
I've been cruising around in the truck, and it's been driving great. No issues with the idle, or misses. Runs like a top!
Since I have a working boost gauge now, I have noticed that the supercharger seems to be making less boost than it should. I'm seeing just a bit over 10psi max, and with the pulley I have installed, it should be closer to 14psi.
I looked through some old posts, and found that the previous owner of the supercharger was having a similar issue. The only thing I can think of that would be limiting the boost would be a faulty bypass valve, so I may need to replace the bypass valve on the whipple. We'll see how it works out.