Hi,
I'd like to add to the conversation here. Please understand that I am a Honda dealer and do feel like I need to be sensitive to that fact and somewhat politically correct. In other words, I'd like to tell you what I think is going on but I'm hoping it doesn't result in a rush to Honda dealers and Honda Customer Service. I'm walking a narrow path here in trying to help without causing issues.
The Honda BF90D (EFI engine) has a bunch of stuff going on in the ECU (Electronic Control Unit). It's programmed for BLAST, for Lean Burn, and for V-TEC (variable valve timing). BLAST senses how quickly the throttle is moved and adjusts the timing for more reponse if it senses a quick demand for power. The Lean Burn technology operates between 2,000 and 4,000 rpm. When the engine is operating in a steady state, and within certain parameters, the ECU will attempt to lean out the engine as much as possible for better fuel ecnomy. V-TEC happens at 5,250 rpm and literally changes the cam lobe the rockers are following to a high-duration, high-lift profile for power.
I had issue with the first of the BF90D engines in trying to get them to "settle down" in the Lean Burn range. Power application was very erratic at the 2,000 rpm and 4,000 rpm mark in particular and not particularly stable within the 2,000 to 4,000 rpm range. I had a Honda engineer out here to check what was going on when we complained bitterly about the first few BF90D engines. The engineer found that the spark advance was changing in ways it shouldn't when moving into and out of the Lean Burn range. I proposed that is was due to the nature of the CD22 hull shape and its (rather) unique power requirements (when compared to more typical hull types) and that the ECU was having trouble "sensing" the load on the engine and when (or when not) to utilize Lean Burn. This resulted in very rough (really, jerky) operation.
Honda did more testing at their facility in Florida and was able to replicate the problem. Subsequently they worked with engineers in Japan to change the programming in the ECU. We replaced the early ECU's and found the new programming to be much better. The ECU also "learns" the typical operation of the boat over time so oft times things improved even further with use.
I've found, repeatedly, on lightly loaded boats (not lightly loaded C-Dory boats but boat that don't demand a lot from the engine like the C-Dory) that it's difficult to get a BF90D to run absolutely smoothly. Or I should say "all" BF90s, for some reason some do run quite nicely. Most seem to have a stumble or surge around 2,000 and around 4,000 where the Lean Burn comes in and goes out (respectively).
In trying to help in this one case I'm afraid of having everyone with a BF90D start wondering about theirs. Keep in mind it was only a very few early BF90Ds that had the initial issue and that stumbling (or surging or hunting) is usually mild and that there are still very good things about the engine that make it worth having even if it stumbles a bit (this isn't unique to the BF90D, I've had $25,000, highly engineered, top-of-the-line motorcycles exhibit the same issues; bikes from a highly regarded German maker that really shouldn't surge...but do).
If you have an issue like this with your BF90D you'll have to make some choices. It is (or can be) annoying and it probably shouldn't really happen but it does sometimes but it won't damage the engine or leave you stranded. You'll need to decide how far to push it (if at all) with your Honda dealer and whether or not it's worth the effort. I can tell you if Honda gets a dozen calls on Monday morning saying they heard from a dealer up in Washington that they might have an issue with the ECU, Honda is not going to be very happy with me at all. I'd encourage you analyze your own personal situation and determine if the level of the (potential) issue is worth the pursuit of a (potential) resolution. If you have a very early BF90D with a very pronounced surge or stumble I might suggest following it up. If you have a later engine and just some stumbles around 2,000 and 4,000 you might decide that, while not ideal, it's fine as long as you know your engine isn't being damaged and you won't be stranded.
Hope this helps out a bit.