Hey bro, I use Ball jars and their smaller brother Kerr jars. Funny that the same company brands different sizes differently.
I second starting the flush now.
When I flush I use DM Zone... it acts as a tank sanitizer, like h202. I'm not necessarily suggesting you get that product... just letting you know I don't do strait water. (my first grow I eventually did, but the plants were acting up and I was trying anyhing). My Purple Kush grow, I flushed using zone (as per directions).
Also about flushing one but not the other... I would see how tangled the roots are... becuase if there are too tangled, the damage you will do to both the plants may not be worth what you would gain by separating them. So the thing to think about is the benefit from separating them (which is pretty minimal in my book... we all have different books), vs. the shock they will receive. Even if it doesn't harm the plants, it may set them back a few days or a week. Not trying to say separating them is a bad thing... but it may be.
Home stretch... i'm pumped for you.
Man if you were that high off the uncured popcorn... imagine the cured big nice tops. Your head might either explode or fall off, haha.