I know you don't like to think about this, but - If you have the 20219 tune loaded, the GiPro shouldn't be doing anything to the timing since the timing tables are the same for 1st - 5th. It's also not doing anything with the secondaries, which remain partially closed in all gears until you take them out.
If you take the manifold off to remove the secondaries, which in my opinion is a royal pain in the ass, put the K&N RU-2780 filters on at the same time. You're going to need to add fuel anyway for the missing secondaries. I find it hard to believe that tweaking the injectors with a Dobeck and listening for a smooth response is going to optimize your tune. With the 20219 tune in there, getting a PCIII with O2 sensor controller and custom dyno tuning it is your best bet.
Tuneboy is only going to help you if you want to eliminate the rev and speed limiters, correct the speedo, and mess with the timing, which I wouldn't recommend.