Help for an amature in getting started.

[Shifty]

Well I think I know what I want to do with it, now all I need to do is get some wire. Would I be right in saying you would wire first to get shape then prune the foliage pads.

[shibui]

I note that you have found that 1 side of your juniper is bushier than the other. I guess that this is because the tree has not been rotated regularly. The side facing toward the light grows stronger and bushier and the side that is more shaded grows less. A very important point to remind us all to rotate all our trees at least every week so they grow strongly on all sides.

Would I be right in saying you would wire first to get shape then prune the foliage pads.

You can do it any way that works Shifty. If you can see what you need prune first then wire (saves time and wire) but some people need to wire first to see the shape then prune after but you may find you then have to prune branches you have already wired - a bit of a waste

should I be cutting right back yo the brown parts?

First, let's be very clear - we are talking about the bark color, not leaves. Answer: It depends.
Some areas you might want a bit longer so leave a bit more. If you want some parts shorter you could cut back into brown bark area (as long as there is still plenty of green leaves left).
It looks to me that this was a well shaped bonsai before it was let go so cutting back all the new (green bark) parts will probably get you back to a pretty good size/shape but you need to make the final decisions about how much to cut and where.