Posted: 11/06/2015 at 07:21
Jade, they're going to end up throttling each other. The toms, particularly, and the chillies are very sturdy and can cope with a surprising amount of root disturbance, particularly at the stage they're at. In fact, one of the reasons for potting up toms is to give the root systems a bit of a shock. It stimulates them.
I'd tip out the pot and go to work. Trace the stems down to the roots and prise them apart with your fingers or something fine and sharp like a knitting needle. You'll do some root damage but it shouldn't matter. In fact, if you happen to sever a root system completely, treat the plant as a cutting. Put the stem into a glass of water or poke it into some damp potting mix and keep it out of direct sunlight for about a week. It will grow new roots.
Successfully separated plants can go into individual pots with damp potting mix, again kept out of direct sunlight until they recover from the trauma. Damp doesn't mean wet.