Some of those things can be purchased from spare parts shops, other parts are going to be hard to find here in Oz.  Atari machines are regularly parted out in the US so maybe keep an eye on eBay.

Plastics can be flattened out in an oven but you have to keep a close eye on them, keep them away from the fan in the oven and as soon as they start to flatten out, remove them and let them sit for a few minutes.  I sit them on grease proof paper on a tray.

Metal parts like side rails and lockdown bar you would be better off looking at stripping them and having them re-chromed, they won't be very easy to find.

Pretty sure the displays are repairable.

Plenty of info on backglass restos.  Typically guys will seal the artwork with something like Krylon Triple Thick clearcoat and then apply any touch ups over the triple thick so it can be removed if you stuff up.  At least you know the artwork will not get any worse on the back then.

With the backbox, was it folding down at all - there may have been a bolt in the base of it holding it in place?

He sounds like a fair old project but stick with it and post some pics of the machine if you get a chance.