Starting to think it may be the Pertronix module/distributor.
Did you ever resolve this issue? I have the a similar setup and am experiencing the same issue. I have a 1987 Mercruiser 3.7L MCM 165 4 cylinder motor. I have the Pertronix ignition on my boat as well. I run the boat for 15-20minutes and then once it's got my boat starts to miss fire and then shutdown. I am then not able to get it started again until it cools. I know this post is pretty old, just hoping you may engender if you resolved the issue.