Don't panic
Go back to your fundamentals. Start with the nebari and the base of the trunk. What does it tell you? Pull the tree out of the nursery pot and remove the top soil until you can clearly see the surface roots. Rotate the tree and look at the trunk and roots from all angles. Ignore the branches. Tip the tree left and right to see if you can improve the line of the trunk. Come up with a design plan based on this process.
Now look at the rest of the trunk. Does the top of the trunk work with your design? Does it have proper movement and taper? If not, can you select a branch to serve as the new trunk line? At this point in your mind you should be able to visualize all the way from the surface roots up the base of the trunk to the apex - seeing the design line and nice taper, movement and character. This is the "skeleton" of your design.
Now look at the branches. Which branches work with the future of the bonsai design? Which are redundant, too thick, or in the wrong location and can be removed right now? Which ones serve a purpose today (sacrifice branch, or just necessary so you don't kill the tree before new branches have become established?) Eliminate the branches that can be eliminated, making sure to consider jinning them since you can always remove a jin later if it doesn't work with your design.
Now selectively prune the tree, making sure you don't eliminate too much foliage in this first round. Focus on eliminating everything growing straight down or straight up, or branches that cross or overshadow each other. Open up the branch structure so it can breathe and get light into the interior.
Depending how far you think you can get the tree at this stage you may also apply wire, or you may simply prune and allow the tree to grow strong before you apply wire next year. It all depends on the quantity of work that needs to be done and how quickly you can move with the tree. Do not do a dramatic repot, branch prune, and wiring all in one session or you risk killing the tree (as a juniper - some other trees handle the stress better).
