Went through the exact same exercise two years ago, and I don't regret it.
Make sure you add a middle hinge to the jamb. I don't regret using the
original frames, and the casing is like new. Otherwise, you'll end up
redoing your baseboards, too.
I find that 5/8" under the door is enough for AC and heat to make it
through. I have HW floors and no carpeting.
Not sure what you mean by square, but the doors are heavy enough to where if
they're not perfect, they'll "fall" open or closed. I had to redo a door by
chiseling the mortise deeper at the top, and shimming out the bottom,
because the hinge jamb wasn't plumb.