and had purchased the JR (Japan Rail) Pass. That pass worked on all bullet trains and JR lines throughout Japan.

What I didn't know, there are train lines that are privately owned (or at least that's how it was explained to me), so they are not part of the JR line system, so you have to purchase a separate ticket to use those lines. Luckily, I had someone with me that knew that and explained it to me. Otherwise, I would have been super confused as to why my train pass wouldn't work when trying to scan in.

If you understand that, simply using google maps will easily guide you around. Only once or twice did I have to ask a random Japanese person which side of the platform did I need to be on. I don't speak any Japanese, but I was able to show them my phone with the directions and they pointed me the right way.