Don't worry, you can get the mechanism out with the window in the up position. You just need to use clamps and or gaffa tape to hold the glass in the up position then undo the 6 bolts that hold the whole mechanism in place.
If you can't get to the trickier 2 easily, then lower the whole shooting match down into the space once you've undone the bolts you can get to, and then with a bit of fiddling about you will find yourself able to do it. I did it in great haste (rain) the first time and not at home with easy access to tools etc, but still managed it.
I swear the hardest part is getting the door card back on. Not fun!
Oh and you will need a good magnetic screwdriver or some ingenuity with tape and/or blue tac to get the screws for the door pocket in and out!