I had that exact problem with a 2000 Ficht 200 a few years ago.
I called Chet at DFI and he said it was the EMM. He explained it in detail at the time, but I can't remember exactly what he said. But basically, the spark signal coming from the EMM was really weak. If yours is the same, that is why it actually runs better with fewer plugs connected.
I was a bit skeptical, and went through everything else, including capacitor, stator, TPS and a few other things, but I eventually sent in the EMM, and sure enough, it has run great ever since. I wish I had just done that to start with.
I sold that boat a couple of years ago, and saw it comeup for sale a few months back. I asked the owner how the boat was, and he said it still runs great, but he wants a bigger boat that is more suited for offshore fishing.
I'm no expert, but I'd recommend you call Chet. He knows the Ficht systems well.