Motorcycle Repair: Baffle drilling on Harley, harley davidson softail standard, screaming eagle pipes

Question
Have a 2003 Harley Davidson Softail standard, I have the high flow air intake, the Software download and finally my baffles open, the question is about my Baffles.

Here is what I did, I did not want to remove the baffles so I adapted a metal home saw 1 1/4 inch in diameter which fits inside the baffle all the way into the end of the baffle cutting out the very end cap out, I did this successfully and the harley dealership states it sounds just like screaming eagle pipes and that they never heard anyone doing what I did... they usually drill out the entire baffle. I and my wife thing I may have overdone it, while I enjoy the sound it is a bit loud when opeining the throttle.

1. Is there a way for me to determine if I have my baffles too open or not? I was thinking about inspecting the color of my plugs to see if they may be too lean (light in color) but can you advise.

2. I was told I had to open up the exhaust when the Stage one download was done with the air filter.

3. I am thinking about getting an other set of stock pipes and redrilling the baffles this time only creating a 1/2 or 3/4 inch hole,

Any comments on any of my 3 concerns above? Please do comment rather than to tell me you wouldn't drill baffles in any way...

Answer
Will I would start by throwing the stock pipes in the can, You hve hert your low end and your midrange horse power and torque, and you have also effected you EFI. and there is not a down load from Harley or anybody else that can tune the bike correctly with your muffles that had been mod by U. Get a set of Cycle Shack PHD 2" stepped duel exhaust and then have a Power commander USB installed and have the bike correctly dynoed tuned by a dynojet certified tech and he will adjust all your fuel needs at every throttle position and at every RPM. This is the only correct way to tune your bike. You will NEVER get it tuned correctly even with a power commander with the exhaust you now have on your bike, The cycle shack is very low price and there is not any exhaust system on the market that will match the horse power and torque accross the entire power band. The down load was a wast of good money!!!. with out a air/fuel ratio monitor in the exhaust there is NO WAY to get the max out of the parts you have or are going to buy.  
Johnny 602-705-7474