I'm a shade-tree mechanic so take my comments with a grain of salt....
I just did the same thing on my '95 Wave Raider 700 and had the same problem. Everything said my ski has 38s but the exploded diagram much more closely matched the 44s. I also have the the Clymer Shop manual and the Yamaha Service Manual. All of the diagrams matched what is described as the 44sbn in your pdf.
Dont know if you did it but I soaked my carb bodies over night and blew out the various galleries and channels. Lots of crud came out!
I followed the 44 sbn exploded view to reassemble. What wasn't documented anywhere that I could find, is the reassembly of the front carb's pulse side that didn't have a diaphragm assembly.
Once I reassembled, it started very quickly. (It had been a hard-start previously). On the stand, it definitely seems to run better. Previously tended to run away, bogged under acceleration, needed ether to start that first time of the day, etc.
Just my humble opinion. I defer to the more experienced posters on this board...
Greg