I had the exact same problem on one of my 1996 Crusader 350's (454ci). Both engines could idle flawlessly all day long, and even under load everything was great for about 15 minutes. After about 15 minutes of cruising, the starboard engine would bog down and not go over 2500 RPM's. I replaced the big fuel filters/separators and did not see any "inline" filters as people online kept suggesting. After the problem was still there, I proceeded to buy rebuild kits for the carbs, and it wasn't until I was tearing it apart that I saw the "inline" filter everybody was referring to.
The filter is not exactly in-line as I would think the term suggests. I was picturing a clear filter with a stone or paper element, in-line with the fuel hose somewhere between the tank and the carb. You know, like you would put on a dirtbike, or lawnmower or something. No, the filter rests inside a large fitting on the side of the carb.
If you look where the fuel line goes into the carb, there is a big fitting. I forget, but something like a 1" wrench will get this fitting off, and you will find a little filter. I will almost guarantee it is clogged up. I put the filter in that came with the rebuild kit, and it runs excellent! Took it 100+ miles on a two day Catalina fishing trip with no issues, plus five or more day-trips since, and the problem has not come back.
For all I know, you may have checked these already and your problem may lie elsewhere, but I wanted to clarify MY confusion for you in case you are thinking like I was. =)
Let me know, and good luck!