I always get some variation too. I think pre soaking the seeds may help because some just seem to germinate sooner giving them a head start, but I haven't tried it. Some cotyledons open at different heights also. I compensate for it by moving the taller ones downstairs to a cooler room and giving them some oscillating fan time while keeping the shorter ones upstairs in a warmer sunnier window location. I add starting mix also, burying the cotyledons if necessary. In time the shorter ones usually catch up but I don't make too much concern of it because I plant them so that only about 4-5 inches are above ground. Don't be shocked if the runts of the litter out perform the others when the season gets under way.
Ken

1-I would say, transplant them to bigger pots, or atleast fill up those half-empty cups.
They need more medium to grow more roots.

2- you can start a second set right now. This will give you a sort of
consequitive planting,ie not all of them fruiting at the
same time. In zone 8 there should be no problem at all.
You can even direct sow tomatoes in the garden, in May.

Well I am glad to hear that the little ones will still be producers, I wasn`t sure if they would stay stunted. I really have had fun starting from seed instead of buying plants, this is my first year and I think its the way to go for me, I love seeing the sprouts and how fast they take off when you pot up. Next year I will have a spare bedroom to convert to a plant nursery oh my gosh I think I am addicted. :o)Deanna