First off, forget the level and get a framing square and check things first. Then measure corner to corner both ways in an "X" pattern. The chances your door is out of square out of all of the doors made the same day, before that day, and after that day is slim. And a rough opening is just that.....a "rough" opening.
One thing you did wrong on a prehung door was to take things apart to see if it opens and closes, because you have now racked the frame. The stops are put in there from the factory for a reason, and that is to keep is square while being shimmed and temporarily fastened. And even if the door is slightly out, you can cheat things a tad with your trim.
Your rough opening has to be a certain size all of the way around. THis allows for clearance of the door to mount it square in the opening, even if the opening isn't square, hence again..."rough opening". You may have a 3/4" gap at the top, and may be sitting tight at the bottom on the same side, and have a gap on one side of the threshold.
You need to find the clips and such that held the door square from the factory, put everything back together so the door is setting solid to the frame with equal spacing, and start back at square one. Don't worry if it doesn't set square in the rough opening, that's what shims and trim is to fix. Right now your trying to fit a racked door frame in what is most likely a racked rough opening.
And get your level checked. If you don't know how to do it, there are videos of it. Lay it on a flat surface, then roll it over to the other surface, if the bubble moves from once side of the vial to the other in the least little bit, your level is out. Hang the level off of a long nail, then flip the level 180 degrees and check your bubbles. Off just a red one, will equal to a large gap from top to bottom of a doorway. If the weather is calm, hang a plumb bob down in the doorway as you won't get anymore plumb than that.
Being a machinist all of my life, one of my largest struggles is working with wood. Most people know what 45 degrees is, or 30, or 60 degrees as that is the most common used on tools when it comes to construction. A lot of tools like your power says have a wide line, to line up another wide line, but may come in 5 degree increments. One degree = .017/inch. Move that 1 degree up 12" and now you have a gap of a little over 3/16". move up another foot, and you now have almost a 7/16" gap. Now one degree doesn't seem like much until you have your two little lines on your saw just a red one off, or that board has just the slightest of twist to it, that most wouldn't see. Carpenters, and especially rough framers work off of a tape measure to lines, then cut the wide pencil lines with a 1/8" wide blade. If you are on one side or the other of the line just a little, if your saw has just a tad bit of kilter to it, if one side of the teeth on the saw is duller then the other side to where the saw doesn't track right, you know have what machinist call a "stackup problem". Or in other terms.....the sumbitch don't fit!!!!!
Doors are made in jigs from the factory, and are fastened in a way that you do not remove the clips and corner boards until you have it securely fastened into your rough opening. You pulled your clips and corner braces, and are now complaining that nothing fits correctly. Get out the sawhorses, square the door up in the frame, put the security clips back in and your corner braces, double check your window while you are at it, send us some pics, and we will fix it for you over the internet.
BTW......not trying to bust your balls, but trying to help you out. Welcome to Garage Journal, and lets see some of the pics of the build and what's going on. We'll get you bailed out of the bind.
I had to walk away because the inclination is to throw the $500 door on the burn pile. It has a solid metal bottom piece, so there is no way that one leg is longer. The adjustable threshold is also at the minimum setting. I made sure that it wasn't out of adjustment. Any suggestions here?
