You did not say if there has been water in that area or not. If water got in there, then the wear will be from rust, etc.
I would also replace the two seals #20
http://www.boats.net/parts/search/Honda/Outboard%20Engine/2007%20and%20Later/BF90DK0%20LRTA%20/MOUNT%20CASE/parts.html and the shift shaft seal #38
http://www.boats.net/parts/search/H...nd Later/BF90DK0 LRTA /SHIFT SHAFT/parts.html
The shift shaft seal has been the source of water in some of the 90's that are not rigged correctly and water is forced up through the seal.
I would also remove the sealing bolts, #1
http://www.boats.net/parts/search/H...Later/BF90DK0 LRTA /CYLINDER BLOCK/parts.html on the underside of the powerhead and seal the washers on both sides with a good RTV or Hondabond 4. These tend to rust and leak oil. If they are rusty, I would replace them.
Otherwise, follow the manual and do not try to shortcut it. On the other hand, sometimes will will tell you to take things off, that you do not really need to take off for what you are doing. Just think it through as you go.
Pay attention to the instructions on putting it back together. Note that most of Honda gaskets go on without any type of sealant, however, you will need to use some in a small section of the mount case gasket (under the powerhead). If I recall, there is also some you will need when reinstalling the midsection.
Be sure to loosen and install/torque the mounting bolts in the order specified in the manual.
So, be sure to read the manual.
One last thing....take a lot of pictures as you take different sections off. Especially, when you have to remove hoses and wiring. The pictures will save a lot of time looking things up in the manual when you need to know what is routed over what. I usually take closeup pictures all around the motor before I start and as I uncover different layers.
Mike