The only reason you'll need immigration is for the 90-day report, and you don't need to say anything about your course. You can expect a whole lot of headache if you plan to do a 180 day extension in Thailand instead of border bounce.
Since the funding is a major requirement why don't you tell us what kind of money you've been playing/surviving with over the last 3 months until you top it up to 500k.
Your possible tax liability is only on money remitted into Thailand. The first 150,000 baht is exempt, and there are other exemptions that you could possibly qualify for.
I second, that handing over a visa printout with passport would have likely informed the officer immediately why you are in Thailand. It's their job to be suspicious. Especially with your entry history. You know what's required and expected, you created your own chaos.
Why would you submit airline tickets, were you asked for proof of location already?
Just to be clear, you applied in Malaysia already and entered Thailand without the DTV being approved? Have you been asked to submit proof of location yet? When did you apply, when did you enter Thailand?
Practically, it doesn't matter when it was submitted at that location. Nothing to fix. Just do your 90 day report as per your situation in person or online.