jdizon, your fitment problem isn't at all unusual. Bronze bushings, whether they're the replacements from Yamaha or aftermarket units, are going to have thicker flanges than the OE nylon bushings. The inner bushing (cylinder) needs to protrude past the flanges of the bronze outer bushings to keep from locking up the swingarm when the axle nut is torqued down, and the extra thickness often eliminates that clearance.
Here's what to do. With a 12" caliper, measure the inner bushing length. Subtract .008" from that number; that's the distance you need between outer bushing flanges to provide .008" of clearance. Measure the distance between the outer bushing flanges and subtract the needed distance. That's the amount of material you need to remove to recover clearance. Remove the outer bushings and remove half that amount from each end of the swingarm with a mill file, measuring with the caliper as you work.