Not familiar with the bomber exhaust but with any restriction your jets would be too big with the 48s. Modern gas does not color the plugs like the old leaded non-alcohol gas did. Makes them much harder to read. Make one change at a time and test. Where you live has quite a bit to do with jetting, your elevation changes your jetting. Disconnect and ground one plug wire and turn the idle up just enough so the bike will run on one cyl. and adjust the pilot screw on the side you have the plug still connected on. Turn the pilot screw in until the engine runs rough then back out until the engine runs rough counting the turns between the 2 points. The correct setting is 1/2 way between those 2 points.I would remove those shims you have on the needles first and start over. Once you have the mixture right and adjustments made if you have a mid range lean spot then add shims or different needles. Each change you make effects the others since they do overlap as the throttle opens. I have straight pipes and pod filters and I run 48 pilots and 155 mains with no shims and my mix is nearly perfect across the board on a dyno. My mixture screws are about 2 turns out if I remember right.
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