Was able to get everything working enough to record some tracks today. The box I used was a bit larger then I would like but it’s the only thing I could find. The tracks came out pretty good as far as accuracy, and it does not appear that it dropped any points. Still do not have the timestamps working so I can’t be 100% sure on that last part. It did create three different files indicating that the main uC reset for some reason, though it did recover.
There is some issue with my GPX library, I think strings have some additional overhead in the new version of arduino which is causing problems. I was working on converting things to using pgmprint and char*s anyways so I will keep moving forward with that. I’m going to add some switches, secure the box some more and try again tomorrow.