I hate that you have to go through all of this ... but on the bright side, you'll know more about the guts of the door than most people on the forum.

My recommendation is to unbolt the glass from the regulator. Get the guides back on the track. Bolt the glass back to the regulator. Run the window up & down a few times before you put the door panels back in place. Don't forget to add more lubricant (lithium grease or graphite) to the tracks before you close it up (this is the rare occasion where "mo' is betta" ... you can't put too much lubricant on our window weatherstrip).

When you unbolt the glass from the regulator, it may be helpful to have a couple of suction cups on hand. Push the glass all the way up & put a suction cup at the front and back of the glass as low as possible. When you let go of the glass, the suction cups should hold the glass out of the way whilst you are working on the regulator. Don't laugh. The drivers side winder on my old Land Cruiser was held closed by suction cups for several years that way (yup, Toyota didn't get their regulator any better & it went KA-BLOOEY ... different failure mode though). It even made it through inspection that way.

EDIT:

You may find that after you get the upper guide back in place, you can do the washer thinggy to keep it aligned properly. With the top guide off, that part of the regulator is being held at an angle which is causing the lower guide to have more pressure on it.