Leave it be.

Don't prune until after new growth is well-developed. Then you'll know which parts are dead and should be removed.

It's been a few months now since my Jacaranda got frost bitten. The branches fell off (along with the leaves). The plant is about 8 feet high and is now sprouting new growth from the base (about 3 feet high bush). Nothing on top. Should I trim the top off to the hieght of the bush or still leave it be.

I would trim off the top to the height of the new growth - try to cut at a slight angle, so any water runs off, but cut such that the lowest edge is no more nor less than about a quarter to a half inch above the highest new shoot's origin on the trunk. The new shoots will probably be a bit brittle, so be careful of them as you cut.

Later in the summer, you can either leave 2-3 of the new shoots to grow, or take off all but the strongest - it depends on if you want a single-trunked or a multi-trunked tree. Be aware that you may get new growth from the attachment points of the cut off shoots for a few years - rub them off as soon as you notice them.

Depending on how well the new shoots grow, you may or may not get flowers in the next spring, but should by the following one.

My main trunk died with the frost and now the branches have re-grown to about six feet tall. It looks more like a bush than a tree. Should I trim the lower branches and thin out the now 6 possible main trunks that have formed? If I should, when should I do this?
Please advise.

Also, should I wrap the tree this winter to prevent more frost damage until it is more mature?
S.

A you have found out, jacarandas don't like frosts. If there's another killer winter while you are still gardening there then you will be left with a sprouting stump (or less) again. Maybe time to move on to some other kind of tree, one that isn't tropical. Otherwise, leave it until next year, think about selecting a replacement trunk at that time. If you have to baby it with something like covering it up to get through this next winter, then maybe it's time to move on to...