You should already be on a marriage Non-O Visa and you will be looking at seasoning your funds for 2 months then applying for a 12 month Extension of Stay, not a Visa. The Kor Ror 22 can be obtained in minutes at your local amphur so I assume your constraint is the seasoned funds unless you were married outside Thailand which means you have not planned this at all well.
Yes, maxing out a Visa Exempt entry to get 90 days then returning soon after for another Visa Exempt entry is a big red flag. Yes a border run agent is always safer.
Your extension will only be issued up to the validity of the passport so, in your case 6 months, then you apply for a new 12 month extension for your new passport, you lose 6 months.