Nate it sounds like you are off to a good start.
You may need more fuel or less timing at the transition point... I had the same problem when I installed W/M. Also you can adjust the fuel trim for each injector to fix the plug issue.
To do this yourself install a A/F monitor...I use the DynoJet model but many others like this:
Universal Digital Tuning Products and Tuning Tools from Innovate Motorsports
and wire it to the VEC.
My O2 sensor is on the drivers side bend just after the collector but others have sensors on both the left and right banks.
Get the software and load it on a laptop (sits on the passsenger seat so you can start and stop logging) and log some pulls.
You can fix that transition issue while doing some pulls to the legal speed limit.
Once you have the logging files you can E mail them to Sean or Joe Dell and they can tweak the tune and E mail a new tune for you to load. Then go for another drive and log some more.
It will not take long to get familiar with the software and you can take it from there.
If you compare the costs of dyno time to... software, A/F monitor, cheap laptop if you dont's have one,a VEC card burner and some wire you will be saving some $$$ in the long run.
Plus you will be able to make cards to drive in various temps and keep an eye on the A/F.
If you need some help on the details send me a PM and we can trade phone numbers.