Just been looking through the extensive Chilton's motorcycle repair manual 1945-84 version because, well, reasons. There's nothing in there that differentiates the studs.
Without any clear overhead images of the head, it's very hard to say what goes where. Other models in the same family (like the 350/4, 400/4 and 750/4) had a couple of shorter studs in the front; the 750/4's were the outermost front (corner) two whereas the others were one in from the front corners. The 650 seems to be the odd-man-out and none of the images I could find showed the top view layout clearly enough.
If I had to take a guess, I'd start with the two rear outer corner holes (carb side). With the exception of a couple of the inner holes, the stud holes at the front (exhaust side) are shared with the spark plugs, so it's unlikely to be any of those. If all 8 of the holes that are only accessible inside the head have the same floor depth (I have no idea whether they do or not), the logical place for longer bolts is in the only two remaining holes, being the outer rear corners. Looking at images of the underside of the head, those holes also have spaces for knock pins.
That said, 2cm is a fair old difference in length and not something that's going to go unnoticed if you get it wrong - those longer bolts should sit up if they're in the wrong place. I'm assuming you've already assembled the engine dry to see how the bolts feel in different locations . . . it should be fairly obvious where there are a couple of deeper holes.