It depends on the style of cage you plan to use and how it is positioned. The most common is the smittybilt style. If you plan where you want the forward supports to go, you should be able to avoid most problems. You should be able to roll the windows down with no interference. You may have some trouble with the wing windows though (they will open, but you need to open the door to do it. I wouldn't move the forward bars in to avoid them, because it will compromise strength.
I have seen several solutions for the E brake. The simplest way is to remove the bolt that mounts it to the dash and bend it out from behind the bar reattach it to the dash. I've had mine this way for several years and it works just fine with no binding.
There are also several ways to do the glove box, depending on how creative you want to be. The cheap way would be to cut off just enough of the door so that it will clear the bar and leave the small opening that was cut. Or you could take the piece that you cut out and mold it into the dash. Or hinge it so that it will fold into itself. I've also seen some sliding hinges that allow the glove box door to slide towards the middle of the dash once it is opened. On the extreme end, I've seen many that have relocated the whole glovebox toward the center of the dash, where the radio speaker is. I've personally gone the WAYYY cheap route by removing the door altogether and losing it somewhere in my garage
For just a standard 6 point cage, you shouldn't have any problem with access to the back seat.
Most of the weld together or complete kit form cages mount to the floor (usually 3- 5 bolts per attachment), and also tie into the bed rails for support.
If you're planning on a weld together cage, you definetely want the final welding to be done by someone who knows what they're doing. Some gusseting at intersections and some way to tie in the floor supports to the frame would be a big plus.
Jason