Schengen was designed for EU countries to do away with internal borders and make life and business easier for EU citizens. However, you are a non-EU citizen.
Passports and visas are for individuals, not couples. Your first concern and question should be about yourself. How can YOU stay in Portugal for more than 90 days with your wife. Forget other Schengen countries for the moment. Portugal will require **YOU to get an extended stay visa.** There will be forms to file and documents to show. Generally, most countries do not allow an extension over 90 days just to "travel", otherwise we all would be getting them. There has to be another reason outlined by Portugal in your case. Don't assume you can stay in Portugal longer than 90 days just because your wife has a passport, citizen card and can.
Another thing is your statement that your marriage was "registered" in Portugal. Were you actually married in Portugal and have a Portuguese marriage certificate or are you just "registered" because of your wife?
Staying longer than 90 days in the Schengen zone is not very easy to do. Not impossible, but the exceptions require a lot of documentation and are NEVER granted because you want to travel longer. I am assuming Rick Steves and crew get a work visa as an independent to stay longer. The average tourist won't have any such luck.
First be sure you can stay in Portugal for more than 90 days. If you get an extended visa, you can always fly in and out of Portugal and visit other Schengen countries during that extended period, but if you get caught, the consequences may not be to your liking,