Be careful washing away the soil from roots because every touch will damage the roots a bit. They really love the washing though because it gets oxygen into the roots. After repotting you will probably see a burst of growth.
I've had the same thing before when you go to repot and it hadn't grown out of the original clump of potting mix. I put it down to either sick plant to begin with or stagnant water in the potting mix.
Don't worry about nubeness. You only learn by asking questions and making mistakes.... I've learnt soooooooooooooo much
Tomatoes aren't as touchy as chillies. They love the really wet and fertiliser laden potting mixes!
edit: yeah what secret ingredient? You can't say that and not give it up