Ross,
It's all part of the fun! Ok, well, this isn't the "fun" part, by any stretch. But I know how you feel, went through all the same frustrations when dealing with your same symptoms. Problem was, when I would change any part of the potential issues (fuel system and every aspect of that, carb any all potential issues with that, and ignition over and over before I went HEI) the problem seemed to be solved... until I was comfortable and miles from my dock. Then, same problem. Nobody wanted to be anywhere near me for a few weeks. And when fixed, I forgot all about it, and loved life again.
I can't say that going HEI will fix anything. But I certainly hope you can get it all straightened out, you've obviously earned some fun time. We will all face issues with these classics. But, that's the price of being unique and having some real style. Yeah, we could throw money at boat payments and repair bills, and have the same old thing everybody else has, and assume that it will mean we can have trouble free boating whenever we like, but I've seen alot of newer boats being towed over the years, and, when we've had enough for a little while, or have other things going on, we can park them and forget about them for a little while, and not have to write a check every month.