I have a 2 Cycle 40HP motor that runs like a top.  Problem though...Last fall I took the lower unit off to change impeller.  When I put it back on I believe I tweaked the vertical shift rod that goes to the lower unit when I reconnected it.  Now I have a 2.2mph when I am in neutral.  I am stumped.  

 

I've never torn a outboard motor apart, but it sounds like you put it back together wrong.

 

What happens when you put it into reverse?

 

Maybe look at this old thread and see if you can figure out where you went wrong.

 

https://forums.iboats.com/forum/engine-repair-and-maintenance/mercury-mariner-outboards/138859-how-do-you-align-upper-shift-lever-and-lower-unit

Not sure if you are referring to the drive shaft, is so, no one person is man enough to do anything to bend it.  Sounds like you didn't get the shift linkage back in place properly and you are not shifting into neutral when you think you are.