Not sure if this will help. When I changed the belt on my 94 years ago, the 2 cam marks lined up but the crank mark did not. Not sure it was a factory ‘mistake’, but what I ultimately did was make sure the #1 cylinder was at TDC (put a straw in the spark plug hole) and made sure that piston was all the way to the top. The crank mark remained off, but the cam marks were matched and the engine turned fine manually with the belt on. I asked here and many said to just line everything up. Had I done that, I might have had interference. I guess in retrospect the proper thing to do would have been to break the crank bolt free and re-align the crank mark. I installed the belt with the crank mark ‘off’ and the engine turned fine and has been running well since then (2017 and nearly 20,000 plus miles)- to this day, I’m not sure why the mark was off as I don’t believe anyone else had been in the bike that deep in the past (I had made a new alignment mark using a special marker in white on the crank so if the belt ever had to come off again, it is easy to align). Is it possible to remove your belt, line up the cam marks, and rotate the crank (very carefully) to achieve TDC, then put the belt on and see if you experience what I had on my 94? On my 2000 for the belt job, all was aligned properly.