Yes that is the mod I'm talking about.
I did it while 600 miles 1st service. I did the mod after reading about it in one of the thread:
http://www.ktmforums.com/forums/duke...-690-mods.html
I cant tell the different because I never rode the bike under full acceleration during the break in period. The purpose of the mod is to allow you to get all the fuel you need under heavy acceleration on 2-3. I believe that the restriction allows the Duke to pass emission regulations which are done while in low speed 2-3 gears. This mod should make a different under full throttle acceleration on 2nd and 3rd gears (does not sound like your symptom).
Now since you installed more open slip on your bike is running leaner, might causing surging. You might consider the following actions:
http://www.monomaniacs.nl/tnt/KTM-69...hrottle-issues
Good luck