If you take your Jalapenos from an indoor grow light and force them into "full sunlight", they can be damaged from "sunburn". The sun can be much more intense than indoor grow lights so you should follow a "hardening off" procedure. Plus, the change in temperature/humidity from the grow room to the outdoors can be significant... so look up "hardening off".
As for the roots, what I say is "Life will find a way" ! (that was from Jurassic Park...Jeff Goldbloom). You can have a pretty crappy start to plants and they will find a way to survive as long as they have the correct environment to survive. Water, Nutes and Sunlight.
I never prune my plants (personal choice) unless I am growing indoors and the plants get too big for the tent that I am growing them in. Let them grow however you like. If your shooting for maximal yield then maybe you could play around with pruning. Too much trouble for me. I just want peppers !!