Answer: You sound so discouraged. Gardening is supposed to be fun!
Plants will grow faster when they are warmer, also if they are fertilized. If you start tomatoes very early they will just be quite tall, also. They should be kept close to the lights, just an inch or so below the bulbs, or they may stretch. Sometimes wafting your hand acorss the tops of the plants to brush them gently once or twice a day can help them grow sturdier, I suppose because it mimics the effects of wind and reminds them to concentrate on sturdy stems. "Leggy" tomatoes are not a complete disaster, either, because you can plant them very deep and the stem will form roots.
Sometimes the plants become stressed for either nutrients, water, cold, or simply crowding their roots in the pot and show signs of it much as you described. If the ones you planted in the ground look good then they are probably okay. If they were too severely stressed they may be stunted, but if they are growing nicely now they are likely okay.
The seedlings on the other hand, obviously have some type of foliar problem, probably a fungus of some sort since they were kept crowded, damp, and a bit dark. It might be a good idea to dispose of them in the trash rather than the compost bin. These aspects of seedling stress are again a good reason not to start them too early, to be sure to pot them up as soon as they seem to need it, and not to start way too many of them! (I know that's hard!)
Starting seedlings, providing all the optimum conditions, hardening them off and so on is a lot of work and effort, but many gardeners take pride in it and enjoy doing it. Every year is different and even experienced seed starters run into problems from time to time. We consider it a learning experience and try to benefit that way when things don't work out as we had hoped. One thing you can do to help learn from your mistakes (and successes!) is to keep a journal -- this record will become invaluable over the years. You got pretty far for a first attempt -- many beginners can't even get the seeds to germinate!
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