Gear linkage alignment

What's the trick to lining up the lower unit gear linkage? I just replaced the water pump and now the motor is stuck in fwd. I can see the linkage is moving when I move the throttle, but no effect. This is on a 2006 Yamaha 50

[jb123]

i put lower unit in N and throttles in N.

I've tried that, but the lower unit is stuck in fwd. I can't get the prop to disengage as I turn the gear staft. any ideas?
Thanks

[jb123]

redrop lower unit as you may have jammed the shaft if it did not align.