Did you start up the engine and try shifting gears? It is easy to be a little "off" netural when reconnecting the linkage. You don't want to gears to "grind" when shifting.
Maybe you should first just try turning the prop by hand and have someone shift gears to get a feel to see if the gears engage correctly.
I learned this the hard way the first time I changed a water pump impeller. I did not pay attention to where the linkage connected when I took it apart and I had to make several adjustment to get it shifting correctly.
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