then yeah, the roots popping out the bottom will only make transplanting more difficult and also damaging to the roots, if the roots are at the bottom of your cups, i'd transplant into larger pots, not too much larger either, i've become convinced by everything i've read here, especially StinkyAttic's threads, that you're better off transplanting several times into slightly larger pots than just doing it once into a big pot, better, healthier roots. i'd also just trim that dead shit off that leaf, i don't know if it's necessary but i do it anyway and it hasn't seemed to hurt my plants. i may be wrong but i believe that dead shit like that will spread down the leaf, if you trim it, it should stop the spread. then, you'll only have half a leaf but it will be healthy.
anyway, toke amongst yourselves

bozo,
peace, love, dope