Okay, that helps some. If your sanding final primer with 180 grit, my first question would be why. Final primed surfaces can and should be block sanded with either 400 dry paper or 600 wet paper. If you used a quality 2K primer, sanded the cured primer properly with the grits mentioned, sealer is not required.
When you final sanded, did you use guide coat. Guide coat will tell you very quickly if you have scratches in your substrate left over from the 180 grit you used when sanding the primer.
If you had bubbles in the existing substrate/paint, that is an indication as you mentioned that there are other problems underneath and I'm glad to hear that you realize that a complete "re finish" is required.
I may not be understanding correctly but, you sanded the primer 1 hour after applying it? If that's the case...stop...primer needs to cure longer than 1 hour before sanding...unless your using a 1K or lacquer primer...which...is not a good product to use...for base clear you need a quality 2K or catalyzed primer.
So, what kind of primer did you use, brand name, mixing ratios, etc. This information will help in getting your vehicle looking better until you redo the entire car...and it is great looking car by the way.
I sincerely would like to help, please post the information to the questions and we will get you on the right path.