What can I do about out of square rough opening for new windows?
Rough openings are exactly as they are called, rough. Yours sounds extra rough though. All rough openings are made to have space to add shims, sometimes the rough openings, because of conditions, can only take shims on one side or the other.

As a rule of thumb I usually do not use no more than 2 shims on a side. If the rough opening (RO) has need for more, I usually add a piece of plywood to bring the opening down where 2 shims will work on a given side. There is no rule that says the plywood has to be the full length of the opening. I also rip my plywood filler 1/4" narrower than the RO material. Dimensional lumber shrinks, and this smaller dimension keeps the plywood from giving you trouble later on.

Edit 12-31-13 I need to clarify the shim statement. The 2 shims I refer to is, per placement. I use what is called undercoursing shingles used in roofing. They need to be made narrower, whether split, razor knifed, or table sawn. You get a lot for the money. The ones in the little packs aren't even uniform in their taper. There will obviously be a number of placements per side, depending on how large any given item is to be fastened.

On the opening that is too small at the top, if it is a non bearing wall, you may be able to remove the jack stud and replace it with thinner material. If it is a bearing wall, a picture would be handy to see what the conditions are. It may be as simple as using a chisel to trim the little you need to get the window in. It may only need a good smack with the hammer to shift the framing enough to get the window in. A couple well placed 12D-16D toenails may help too. Give it a whack, literally. 

I can't determine anymore to do without seeing the conditions. Bearing, non bearing, jack studs, common studs etc...

Also check the ends of the wall that the windows are in, the wall may have racked, which in turn will make your ROs out of square.