I had these same symptoms after installed;
velocity stacks, pc111 usb ex (with perfect install), coil relocation plate with dyna coils, new plugs and wires, throttle push and pull cables, ais block off kit, and a bi xenon HID light.
I did all of these at once and when I put it all back together I had to adjust the idle cable way up to keep it running but it ran like crap. erratic idle, back firing, coughing and popping. I spent a few days triple and quad checking everything.
I pulled the spark plugs gaped them to .030 and turned idle cable all the way down and then two full turns up and my bike is running better than it ever has. when i pulled the plugs they were fouled (way too rich). I also synced the throttle bodies