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I'd probably leave the lid on but actually remove the upper half of the bottle a few times a week and expose the little plants to a bit of wind / draft, as this makes the stems stronger.
This really helps with chili plants I've found; with tomatoes, where you're going to tie them to a support of some sort anyways it probably doesn't matter really.
thats awesome, must be the good vibes.
if you split them up now before the roots get tangled and hinder any future growth when you try to repot them, they will grow a lot better and faster.
also water them daily, they like soggy soil at this stage. might be why they took a little while to get going.
I've also found if you get a 2ltr water bottle, cut it in half and put potting soil plus a plant, water it, cover it up with the other half of the bottle and it will have its own little green house. doing this it will grow super fast. only just figured this one out but the bottled plants have been growing about 3x more than the others I've grown this year.