Yes, you have to step on the clutch to start the vehicle. This has been a safety requirement for US vehicles for quite some time. I'm surprised the '97 jeep didn't have it.
You can shift into reverse by accident. Well, it won't go in, but it will grind. The shift pattern is a bit wonky. To avoid any concerns, when shifting from 5 -> 6: while in 5th gear, push the shifter to the right first, then pull it straight down into 6th. You'll find this removes any possibility of engaging reverse.
Unfortunately, there's no quick way to remove the rear window. You have to deal with the small opening.