UPDATE
So I stopped up just before closing yesterday - no more phone calls!
Not happy but at least I have the real story now.
I went right to the manager, who knew who I was before getting my name out. He tried giving me the same ol BS of, oh it's almost done, just have to blah blah blah - I repeatedly said "that's what I've been told for WEEKS". I asked to SEE the bike and he took me back. The mechanic was in the middle of working on it - the engine is back in but everything else was off. Turns out he broke a water manifold putting it back together and has been waiting for that to come in all this time. He showed me the bent pipe, said it started leaking coolant and said it was supposed to be in the middle of next week - everything else was done. The mechanic was real cool, no BS, shared everything he had. The old tranny parts were right there on his bench and we went over the gears, he showed me the rub marks. The manager tried giving me some BS that it was caused by ME resting my toe on the shifter. I quickly squashed that CRAP and he then backed off and said, oh, well, that's just what YAMAHA said it was. Yeah whatever, that's why they immediately said replace everything right? Right.
Then the Mgr blames all the communication problems on his service guy I had been speaking too, throwing him under the bus by saying he's not mechanically competent and doesn't know what to tell customers when they ask. Didn't even know what to say to that.
And just in case anything happens in the future I have the whole meeting voice recorded.
I have now made payment #3 with no bike.