There are also a couple of areas at both ends with light showing between the strips with no evidence of distress to the fiberglass. I thought I had all the cracks filled pretty well. How do I fix this without creating three more problems? Or should I leave it alone?
Light shining through the hull or deck isn't that rare in strip builds. As long as the gaps are filled with epoxy (not air) I wouldn't worry about it at all.
The picture of your problem at the stem isn't clear enough on my computer for me to see any details, so I can't comment on that. Do you have internal and external stem pieces? In other words, what is behind that crack?
It is possible to cut through the glass into an air space between strips and fill it with epoxy; I've done that once. It's easier if you arrange the boat to let gravity help you, and use a heat gun to try to get the air out of the void so that the (less viscous) epoxy can run in. Then you need to add some glass, so I wouldn't do it unless absolutely necessary. If you haven't joined the hull and deck yet. working from the inside is a lot easier.
What is a problem cosmetically isn't always a structural concern - if it's in that category, I would just keep pushing to completion and just 'avoid that mistake on the next build'. That's often my attitude.