I had this same problem on my wife's Sportster. I went through all the basic troubleshooting steps and finally found it had a very small tear in the vacuum diaphragm on the throttle valve. It would stumble when any abrupt throttle was applied, but when I gradually rolled on the throttle it would somewhat respond.
I replaced the diaphragm and the bike ran great. If you rejetted the bike when you put the Hypercharger on there then you easily might have torn your diaphragm OR it just may not be seated correctly. Check that first.
If you need help, just ask.
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