The pipes are definitely holding the peak power back. But, as you've noted, as you remove the back pressure to gain peak numbers the 2700 rpm area starts to suffer (baffle removed). The single stage true duals will not allow higher end/rpm numbers so there really is not a great concern to go after those numbers. Tuning the low/mid will give better usable results.
You're also facing a a typical carbureted tuning situation. Since it is a signal based system, it relies heavily on the exhaust to create those signals (as evidenced by the "flip" in the fuel curve when the baffle was removed). As is often the case, a good compromise between the front and rear cylinders may give the best overall power/performance. I.E. a slightly lean rear with a sltighly rich front. It also becomes a compromise in fuel curve, down the rpm line, where a rich condition at 2500 may not be completely tuned out due to a lean condition at 4500 going lean to the point power drops. Adding two degrees of timing to the rich cylinder, vs the rear, can also help (if the igntion system allows this).
A tip with the Mikuni is to aim the accelerator pump nozzle to favour the lean cylinder (in your case the rear), the residual fuel can find its way well into the fuel curve, down the rpm line.
Its all about the best balance.