2005 F250 Loud shifting after water pump replacement...

Just replaced the water pump impeller on a 2005 Yamaha F250 Four Stroke. I marked the shift splines when I took the lower unit off to ensure that it was in the same position (neutral) for re-assembly. Everything went back together fine but now there is a loud cluncking and grinding noise in the lower unit when shifting and it is difficult to shift. The noise is both N-F and N-R. It wasn't noisy before. Took it apart and tried realigning it several different ways, also played with the cable adjustment to no avail. What could be the problem???

[boats.net]

If had difficult getting lower unit to go all the way up may have damaged shift shaft. Make sure shift linkage on motor is exactly in neutral position as well as gearcase before assembling lower unit back on. If changed gearcase oil may not be full enough.