Hi, I work on the smaller Hondas but your shifting system looks similar in nature to those. It sounds as if you may have "flexed" the extension case, when you hit, enough to possibly bend the shift rod just a bit. No worries though because you can probably adjust it to get it "back in the zone".
Look at items #15, #11 and #39 in the link below.
http://www.boats.net/parts/search/Honda/Outboard Engine/2005/BF40A5 LHTA /WATER PUMP/parts.html
That is the upper shift rod (#15) coming out of the power head and the adjustment nut (#11) and the jam nut (#39) that keeps the adjustment nut from moving.
The following assumes that the boat is out of the water on a trailer in your driveway with the kill switch key removed.
If you shift the outboard to reverse and look at the front of the extension case just below the swivel, you should be able to see and access all three. CAUTION! turn the prop slowly by hand while "dry shifting" the transmission or you could create more problems. Do not get forceful with the shifter. It usually takes one guy turning the prop and another to work the shifter.
Take a good look at the shift rod and nuts and see if you see any obvious damage or bends in the rod. If you see that the rod has an obvious bend in it, try and straighten it as best you can. If this is the case, and you can get the rod reasonably straightened out, stop and try running the boat to see if you've corrected the problem. Also, Verify that the jam nut is tight up against the long adjustment nut and that it has not been moving. These nuts are frequently left too loose after a water pump replacement and will allow the shifter to get out of adjustment. If you find that the jam nut is loose and there is a possibility that the adjustment nut has been allowed to rotate then you need to do a "by the book" shift rod adjustment. That means that what is written below WILL NOT apply.
If you do not see any obvious bends in the upper shift rod and the two nuts are jammed tight together then try the following:
Using two open ended 8mm wrenches, loosen the jam nut while holding the long adjustment nut so that it doesn't move. Back the lock nut down and away from the adjustment nut 3 to 4 turns.
NOTE: This is NOT a "by the book" adjustment. Since you are having problems with reverse and not forward, I'm simply going to explain how to try and mitigate that problem.
Mark the long adjustment nut and shift rod with a Sharpie so that you know where you started. You may need to go back to that setting if this doesn't work. Rotate the long adjustment nut COUNTER CLOCKWISE or to the left one complete turn. If it moves down toward the jam nut, then you are doing it correctly. If it moves up, away from the jam nut, then simply go back to your starting mark and rotate one turn in the opposite direction so that it move down toward the jam nut. Now that you know you are moving in the right direction, turn the long adjustment nut an additional turn counter clockwise. Now Hold the adjustment nut from turning and turn the jam nut so that it contacts the adjustment nut and lock them together with the wrenches.
Now you can put the outboard in a trashcan full of water and run it and shift it to see if the grinding went away or you can take the boat out for spin. Your choice.
Hope this helps and good luck.