Guessing since you are replacing it with a manual kit that it is electric? You MIGHT be able, if you can access the gear mechanism, to take the window carrier off the scissor assembly. Then you can just pull the window to the upright position. Of course it won't stay there however, so not sure what you can do after that.
Perhaps you can disconnect it from the scissor assembly and then pull the scissors to the upright position and then reattach it to the window carrier? That wouldn't work on mine however, window must be down to close the rear gate. Not sure how it is on other models.
1977 Cherokee Chief Levi's Edition: specs to follow investigation.
2002 TJ Wrangler "APEX" Edition 4.7 Stroker, 4" RC Lift, 33" Toyo MT's, SmittyBuilt Front Bumper. More to follow
1974 J-10 258, T18/D20, D44 F/R 4.10 gears and LSD (No... not that type of LSD)