Identically setup bikes may run different jets. Go figure. If your bike wasn't loading up with the 48s then leave em alone till you get your midrange dialed in. Since you didn't take off the carby tops, how do you know the needles don't have any shims? I'd start with one shim. Then go to two. If you need two shims think about a set of TBS needles. Once you have the midrange working double check your mains. Then see how many turns out you are with the air mixture screws. As a rule of thumb, less than 2 turns out then drop the pilots down to 45s.
Generally, the way you jet is to dial in the mains first. Then the midrange, then the pilot circuit. I'd leave the pilots alone for now. Given your selection of 135's and you having what appears to be a major flat spot you'll need to dial in the midrange before worrying about the pilots.
More learned folks than I abound on this site. They'll continue to chime in.
