The custom shop is exactly that... Some level of hand built custom, made to order typically. Usually a different barrel manufacturer and higher grade wood. Super grades are usually just one level of wood upgrade from the sporter, plus a crossbolt and different sling swivels, but they come off an assembly line. I still like them and they tend to run pretty heavy as it is.
Depending on whether you are collecting/investing/speculating or looking for a hunting rifle should probably dictate which rifle. Sounded like you planned to hunt it, so buy a Super Grade. Or just buy standard sporters and upgrade the wood (which is what I've done with two) or look for the sporter and featherweight deluxe models from 2008, which have nicer wood.