Put the overnight stuff on hold for a second... but lets say you started the day with $5K, you're saying you purchased $5K worth, closed them at some point, and then opened and closed some more? (before the overnight purchases)
I'm pretty sure you're gonna get a good faith violation for each of those trades you opened and closed that occurred after the $5K was reached. If this is the case, you probably won't have any daytrading buying power tomorrow.
If you didn't do 3 round trips after the $5K, those funds will be available tomorrow, but only for positions you hold overnight tomorrow. If you did do 3, and their system catches it tonight, then you're under the 90 day restriction and those funds won't even be available to buy something to hold tomorrow night. They'll be available Thursday, but henceforth you'll only be able to buy and hold overnight with settled funds. If you start the day with $5K (assuming your in the 90 day penalty box), and you do $4K worth of daytrades, you'll only have $1K for an overnight purchase.
That's the way it has always been, and unless options settle instantly now... which may have happened, pretty sure that's how this will play out if you did in fact open and close positions after you exceeded your starting balance. Hopefully you didn't do 3 more.
Edit: now there is a chance that maybe they will only hit you with one good faith violation, not 100% sure if it goes by the number of trades, or the calendar date. In which case, you won't be in the penalty box, but those funds still won't be available to daytrade tomorrow.