2007 330 Excalibur 5.7L missing / running rough

[MichaelD]

A week ago, my 2007 216 with 5.7 330 Excalibur engine (700+ hours) was running extremely rough from ~9mph - 40mph, and wide-open topped out ~4400 rpm.
I replaced PCM FCC# RP080026 & also removed & cleaned the flame arrestor several days ago.

Immediately after the FCC change, I was able to get 4,900 RPM wide-open out of the boat ( I've never seen 5,000 ) and it ran well at ~34mph slalom speeds ( no skier ).
I then tried running it in kneeboard & wakeboard speeds (~9-20mph), and the engine is still missing, but not nearly as bad as pre-FCC filter change. While still out, I tried a 2nd run at wide-open, and it only got to ~4,700 RPM. I also tossed in a can of BG 44K to attempt to clean fuel injectors.
Now, I'm also detecting an occasional miss at slalom speeds, but not as noticeable as the slower RPMs.

Today, I replaced the Fuel Pre-Filter Kit ( RP077014 ), and there was some gunk in the old filter.
Engine still runs rough / misses after the pre-filter change (changed ~4 days after the FCC filter)

Did I replace the filters in the wrong order, and do I need do a 2nd FCC filter replacement?
Just trying to think what could cause me to loose 200+ max RPM in under 15 minutes after an FCC change.

The following are "2007 Factory Original". Would it by worth my time & money to change any of the following on a 14 year old boat with 700+ hours?
- Spark Plugs - RP030010 ( I have the original 41-993 with 700+ hours, not the newer 41-101's )
- Spark Plug Wire Set, 5.7L EXCALIBUR, PCM # RK120018
- Rotor Excalibur motors R103011
- Distributor cap GM EFI RA108009

While I've seem some forum posts where people claim to change these every 2-3 years, they aren't in PCM's recommended routine service.
Is a rough engine that doesn't get completely better with a FCC filter change a trigger to replace these parts?

The spark plugs visually appear fine with light gray, and no black soot (like I commonly saw on older-model 2-cycle PWCs).

Any other things I should do to troubleshoot or check for a rough running engine?

Thanks!

[shag]

You still have the original spark plugs and distributor cap/rotor? That has to be a record. I put new plugs in every year. It is an AC delco plug so you don't have to pay for the PCM plugs. They don't even re-brand them, they just put an AC delco plug in a PCM box and more than double the price. I can almost guarantee that its your plugs, then your cap. I bet the electrodes are almost gone on these plugs. Post a pic! I also use ethanol free all the time.

[MichaelD]

Here is a link of an album of the plugs when I pulled them on Wednesday: https://photos.app.goo.gl/skKua7ZDtQQ61Zjs8

For the 1st ~10-11 years (except for ~3 months when ethanol was introduced to retail pumps & I knew better), I've run 87-89 E0 gas. A few years ago, my favorite ethanol-free gas station near the lake changed ownership, and I started hauling ethanol free 89 gas in from a station in Raleigh NC (a bit longer than I want full gas cans in the car). I had problems with missing last summer until I found a different station with ethanol free 93 gas. This summer, I started using yet another station in South Hill VA with 90 ethanol free, and the problem came back. In both years, the boat has run fine with 93 gas that sat over the winter, but when I introduce the 89 or 90, it runs rough.
I'm trying to burn what is currently in the tank before reintroducing 93, also hoping that could be a cure.
Buying 93 feels like burning a Ben Franklin over the course of the summer on a boat that is spec'd for 87.

Sounds like time to place an order for Plugs & Distributor Cap + Rotor from White Lake.
Re plug pricing: After WL's Planet Nautique discount, the cost difference in PCM packaged plugs vs auto parts store prices for AC Delco 41-101's is <$10 for the set. Let me know where you're getting plugs for ~$5/plug because I'm seeing $8-9/plug online.

[shag]

Those plugs aren't terrible and I'm surprised they look as good as they do, but I would replace them. Maybe the humidity here in Fla makes it worse. As far as the pricing, I had found them online the last time I bought some, just have to search a little. I think last time I bought 4 sets of six, and it ended up being cheaper somehow. (3 spark plug changes) and keep them in the house until it's time to change.

[shag]

I also had an issue a few years ago where I had got a bad cap (new, from PCM) and had to replace it. I think they had a bad run of some at one time.

[MichaelD]

On Saturday I replaced the plugs. ( I checked gap & PCM had already correctly gapped to 0.06).
Took the boat for a spin & the missing had narrowed to 12-15mph & not as often.

Next replaced rotor, cap & plug wires (which also included coil to cap wire).
Boat is finally running great! ...and for the first time ever, I saw 5,000 RPM on the engine, exceeding the 4,800 max I previously had since Day 1.

Yes, I did see a merchant on Amazon selling a 6-pack of plugs a few bucks cheaper, but as I need 8 & only plan to do this service every 500 hours, I opted for the ones from PCM