I'm assuming you have a Delkevic Megaphone and you removed the inner baffle? If that helped then you are probably too rich, although from the symptoms I'd guess too lean???
Just a guess though as I'm comparing it to my problem. I'm on the stock jets with my Delkevic but I still have an airbox. I was going to shim the needles yesterday to see if that helped the transition at around 6500rpm but I noticed one of the sliders was stuck. I freed it up and cleaned it and will see how it goes later today.
If the problem is worse at around 6000-6500rpm then you my want to shim the needles and see if it gets better or worse. From what I understand above that rev range the slider should be fully open, so if it's running well there then your secondary mains should be OK. If you shim the needle it will open a bit earlier and you'll be a bit richer for the transition (or rather, the needle will be further out at lower revs).
Someone please correct me if I'm spouting BS - this was the result of a long conversation with a neighbour.