If you don't change the diameter of the wheel tub or raise the wheel tub up into the body you should be able to have funtioning rear quarter windows. Most mini tubes just replace the inner half for added tire width. If the outer half of the wheel tub is replaced it is unsually done with the rear quarter panel off due to the fact that if one has rust then normally both items do. You then have room to work and do a quality job. With out the outer quarter off that will be a tight and difficult area to work in. I would be using a plasma to carve out the old outer tub in peices. But putting the new tub back in will be even more work as this is not how the car was built originally and may not be feasable. Are your outer quarter panels in real good shape??? If not I would start here. Do a search on mini tubes and you'll find lots of info and pics like this
https://lateral-g.net/forums/show...highlight=tubs or
https://lateral-g.net/forums/show...t=15008&page=2