I have a similar problem with my bike. In my case, there is clearly a leak of some kind that is letting air into the line. Mine started after a few thousand miles with symptoms that basically came down to the lever being closer to the bar than normal after the bike sat for a few hours. After a few pumps, the lever would return to the normal fully extended position. If I didn't pump it, then engaging first gear and attempting to move would be problematic. I solved (or so I thought) the problem by thoroughly bleeding the system so that all of the fluid was exchanged. I needed to tie the lever to the bar overnight to get the last air out. After that, it was as good as new.
Now, some 3-4K miles later, the symptoms have returned. Yesterday I bled the system a little. I noticed that there is some paint wearing out on the master cylinder body just below where the cap sits on it (indicating brake fluid contact over time). I made sure to shape the rubber seal to fit the rectangular opening when reinstalling it. I can't see any other evidence of a fluid leak. I also wrapped the slave cylinder bleeder's threads in teflon tape to maybe make the seal better there. I checked the 2 joints where the rubber hoses join with the metal pipe in front of, and below, the gas tank. They seemed snug. There is still some air in there, so tonight I will be tying the lever to the bar as I did last time. We'll see if that does the trick...and see how long that lasts.
Try the same on your bike and it may solve your lurching engagement in first gear.
Please spare me comments about why didn't I take it to Yamaha for warranty service. They would have just bled it like I did the first time, and that would been considered a resolution (I thought it was). It's out of warranty now, but I can bet that it would have just gotten bled again anyway.
Any suggestions on what to look for as a possible cause?