Tony

You can pluck the dry needles off I you want to, it will cause no harm one way or the other. As for what caused them to brown in the first place, it could be many things. The tree should be grown outside. The low humidity in the house will pull moisture out of the leaves and cause them to brown. How much of the feeder roots did you remove? Most of the time you can't take them from a nursery pot right into the proper size bonsai pot because there won't be enough fine roots close to the trunk. It could also be a watering or pest problem.

Tony