Sounds like you bought clubs without first trying them out!!!
Heavier shafts should lower ball flight as would a stiffer shaft if all other variables were equal. So first thing first, replace the S300 with S400 shafts, actually I would just take your 6i or 7i AP2 and swap out the shaft and make sure you have the same SW (and same length, lie, and loft) on both your old 6i CB and your new AP2 6i. Then hit the range and re-evaluate.
Surprisingly you decided on the AP2. Did you get fitted? I too came from the 690 CB's, after getting fitted we decided on a mix set. 4-5 AP2 and 6-9 CB. My old shafts were DG R300 and now I have the DG SL R300, since they are lighter I can swing harder to get more distance out of them... and easier for me to swing.
As for you, I think you need to copy your old shaft specs. If you were getting good results with them before... stick with them.
I would go get fit. I had the same problem with my AP2 then decided to get fit they were 6 degrees off. Needless to say I'm killing the ball now without adjusting per club.
Thanks for the advice. I was not fit, they were a present.
Wow cool present! Then you can invest on the shafts that fits you... cheaper than buying a new one again. I don't know if TItleist can do that for you... if not then just go to your favorite/trusted golf shop.