Charlie,
You are very diligent to try to measure individual cylinder exhaust outputs. Please post whatever you are able to determine as a result.
What cam are you using? If it came with the crate motor, it may not be ideal for the Webs, and all the tuning in the world won't get you where you want to be.
If you haven't already put your car on a dyno, it might be good to do so before you make all the changes, just so you have a base-line for comparison purposes.
The spacers are impressive. IF they make a significant difference other than in ease of tuning, that would be worth posting as well. Good luck.