A few thoughts:
My last engine was a 2002 version of that engine. I will say that it was consistent. First of all I didn't run it very often. Like once every month or so. I did keep the batteries onboard charged. The engine seemed cold natured first start of the day. After that it would start faster than you could get your fingers off the key. Yes I went through the textbook starting procedure like I have done for the past 50+ years.
First hole shot of the day and it coughed and belched (seemed to be running on 2....which 2, I could never determine) and all that and by the time I was passing 35 mph it decided all 3 were in the game (I think it warmed up sufficiently) and it took off. No problems the rest of the day. I could hammer the hole as hard as I wanted to, trim in or so far out it would blow out on plane out.....makes for a faster hole and more fun, and never missed a lick, winter or summer.
I spent a lot of time researching the problem and never came up with a concrete smoking gun, except for early on I found a thermally sensitive CDI that wouldn't fire at room temp but after it warmed up, like the time it takes to get out of the no wake zone and punch out, it would connect. I will say that I probably caused the initial irregularities with it because I ran a 24P Ballistic XP stainless prop which at around 56-5800 ran my 17'+ rig right at 50 gps. So, even though I ported the prop for a better hole shot, I was loading it up pretty good hot or cold engine. I had a 21P Ballistic and it didn't do it but it wouldn't get the top end without running up over 6k and I didn't stay there very long and only used it to prove to myself nothing was wrong with my engine. I kept Sea Foam in the fuel and the inside of the engine was clean as a pin running Penn. syn blend TC-W3.
If you spend a lot of time trolling what you can do is to tilt "out" till your engine is in a "high trim" attitude forcing any unburned fuel mix forward where it can be combusted rather than pool at the rear of the cylinder. That has worked for me on numerous engines and back when Mercs were painted off-white, they came out with the fisherman which was built on that principle.....the whole engine/midsection/lower unit was tilted forward and it apparently worked....worked for me, and slipped over logs easily too.
