If you are going to do elite you better do it soon-ish. They are getting rid of the current offerings and likely raising prices on whatever will replace them. The deadline to sign up under the old (current prices) is September 15th. The deadline to extend from 5 to 20 years if you already have the 5 year is August 15th. Official announcement coming August 3rd according to Thai Elite.
They have a small testing clinic in BTS Thong Lo itself, called Care Box or something. Girlfriend had her PCR test done there before we went to Japan a few weeks ago. You should tell them it's for Japan specifically, as Japan has things they want listed on the test results (such as whether the swab was oral or nasal or both - some results don't list that).
You are thinking of 90 day reporting. An agent can do that for you. But if you stay in Thailand 1 year on an elite, you need to go to immigration in-person (cannot be done through a agent), pay 1900 baht, get another 1 year stamp. Source: I have this visa
If you actually stay for the entire year, yes you need to go to immigration and pay 1900(?) baht to get another 1 year stamp before the original 1 year stamp expires, otherwise it's overstaying. You don't need to leave Thailand (but leaving & coming back would reset the 1 year + save a trip to immigration).