The school gave you what was needed to take to Immigration to get the visa but you chose to go to an agent so that is why the school wanted no involvement. You have learned the hard way.
Because of your age (over 50 I guess) you can purchase a Non-O Visa which gives you a 90 day stamp on entry to Thailand and no need to visit Immigration while you are there
For retirement you need 800k for 2 months before applying for your 12 month extension and maintain that for 3 months into the extension. The minimum then cannot drop below 400k for the rest of the year of your extension.