#48 pilot jet is just plain too frickin big.
What float height have you set for your carbs. 14.5 or 12.5mm? I'd recommend 14.5mm and either #38 or #42 pilot jets.
How old is your air filter? Either get a brand new one from Honda or use the UNI, NU-4055. For the latter, get the UNI service kit for it, too.
For the exhaust change, raise the slide needles, 4th clip position from top of needle, and go ahead and use the #98 mains.
Vacuum synch the carbs.
Put in new clean D7EA plugs after engine warm up and at the test track start position. Start and use full acceleration up to top speed. Hit the kill switch and, pull in the clutch and bring the bike to a stop. Pull all the plugs and take pictures of them to post here.
Cheers,