For about 10 years now I have what I think is a Japanese juniper planted in a hollowed out feather stone (lava rock). It has done ok  but now I want to make it into a Bonsai. The first problem was getting it out of the rock as it adhered to to it so well and become root bound. Next I have this large tap root that I think should be cut off as I have seen that done on Youtube. I think that would be safe to do on a juniper. I also have these above surface roots, should I cut them off, plant the tree a little deeper or maybe try to loosen them enough to pull them down. It was planted kind of like a root over rock style before. These roots are also not going in good directions. Last I have a split trunk or a y shaped trunk. I would like to  get some input on what to do with this. I could jin one side or try to pull the two branches closer together and cover some of the trunk by pulling a couple of branches forward.  I temporarily re potted it in a 2 gallon pot until I can make some decisions.   

I have been told to only allow one "insult" to the tree per year, so if you've just repotted don't immediately wire, prune, etc and to wire in late fall or early winter.