aamert, you are in a tough spot here. Most contractors that care about the work that they do will not want to touch someone else's botched installation. My fear is that anyone you find willing to do so, will be more of the same. Unless these are some highly regarded, high quality/price windows, you may have to consider replacement to have better odds of getting it done right the first time... I don't want to sound like a window salesman in recommending that, but I have encountered similar situations on numerous occasions and from different perspectives, and they always seem to end up the same. What you are asking for CAN be done, it will just be very difficult to find the right person to do it.

This could Be a real difficult job if they have nail fins, the siding and trim interior trim could pose problems as well. Things would be a little easier if they are inserts. A small mom and pop shop would be youre best bet.

I would have no problem doing that job if business was slow but things are moving right now.

So, What I am hearing is that getting the windows replaced will be the best option. However, I do not want 'replacement' windows. I want something that is installed correctly between the siding and framing and flashed, leveled, squared, plumb properly.

It sounds like you are looking for a full frame tear out installation. If your existing units are pocket replacements, that is one more reason why new windows will be needed... They will be sized differently. Be prepared for this to be a significant expense. You mentioned that "brick work will need to be done as well". That is not typically necessary unless you are altering the RO size or shape, but if for some reason it would be, that will add $$$ as well.