As I noted already, I doubt your problems are due to the main jet but are attributable to the jet needle. Only focus on getting the one area fixed. By swapping main jets at the same time as modifying the jet needle position, you will only confuse the issue; especially since the main jets are allowing you to pull well at the top. Once you get the hesitation issue fixed, then tackle the main jets to see if they are actually a bit rich as I suspect.
What pilot jets are in the bike? The pilot jets affect mid-range just a smidgen and it might be possible to increase the pilot jet size a bit by some trickery and help solve the flat spot but first do some experimenting with the stock jet needles.