I have a 40 hp 4 stroke honda outboard. it is long shaft, can I remove the 4''spacer to shorten, or is better to just raise the motor.

I assume you have a 25inch motor, this would be an extra long, a 20 inch is cosidered a long shaft. If there is a spacer and the motor was a 20 inch originaly and was turned into a 25 inch with a kit that would include shift shaft/drive shaft/ water tube extensions then you could remove them and reinstall the gearcase and have a 20 inch motor.
Take the gearcase off and look for extensions, if it just a one piece shaft then it is factory and moving the motor higher on the transom is your only option.

Thank you, Larry,
So I'm pretty sure this engine came from factory extended, Serial or model numbers won't tell us whether shift/drive/watertube is long or extended??
Is there anything I should be worried about when dropping the gearcase to determine? Thanks again, Richard.

No, serial or model will not tell you, it probably has bf40a for a model number, the only way i would be able to find out is by looking it up at work and we are no longer a Honda dealer so I have no way to do that.
The removal of the gearcase is pretty straight forward, 5 bolts and drop it down, just be sure every thing is lined up when you go back with it (shift shaft and water tube).

I have a honda BFP9.9D 2005 vintage. I am I the process of removing ethanol residue from the carb. When I get to the accelerator pump I find a check valve ball and an internal snap ring in the bottom of the chamber. There seems to be no groove for the snap ring and I can't find any reference to these parts in any shop manuals. Any advice?............Dick