No you are not over cautious. Actually, you are quite meticulous. Good finds and you are being pro-active for a fix before they become a problem.
Not so sure about the bubble, but you are doing the right thing getting it check out.
About the sealant? It's not really recommended to remove the old sealant. Just clean it (check youtube.com, lots of videos on this), and re-caulk the cracks. Removing the old could cause more problems, so you just reseal the cracks in the calk.
Congrats on your new purchase.
Here's one of many youtube videos that shows how to take care of your roof, calking, and how to do it. Really simple:
Click here.