Some of these questions have been answered but I'll include them here just to have everything in one place.
The Craftsman 12" manual attached above is for the 101.28900 and 28910, not for the 101.07403. There are enough differences that it may in some cases be more confusing than helpful. You will need to first make a donation but then you can download the parts manual on the 101.07403 (after reading the Downloads instructions up in the Sticky area). The 28900/28910 replaced the 07403, 27430 and 27440 in mid 1957. Some of the parts remained the same but many changed. Atlas (unlike GM and thousands of other companys) never changed an existing part number unless there was a significant change to the part. In most cases, if revisions were made to a part and the changed part was backwards compatible either directly or if some other parts were also changed, the revised part kept the original base part number but got a suffix letter beginning with A, then B, and so forth. When the 10, 10D and then 10F lathes came out, in most cases the base part number was retained but the prefix was changed to 10, 10D or 10F if the new part served the same function but wasn't interchangeable. Atlas bought Clausing in 1949/50. But by 1957, the Clausing people had or had begun to have the upper hand and the only part of those rules that the followed was that if the parts usage changed but the part hadn't changed, it kept its original part number. But if the part was changed it got a new Clausing part number, which I have never been able to determine the logic to.
Anyway, if the part in the 28900/28910 has an Atlas style part number, it is the same as on the 07403. If it has a Clausing part number, it is different. And one improvement that did appear with the Clausing parts lists is that commercial parts like nuts, bolts, keys, etc. were included and sufficiently described.
1. If this is a socket head screw as it appears to be, it isn't original as the original was a Fillister head Phillips screw. But in any case, it plus the other two plus three square nuts retain the 10F-11 Gear Case on the back side of the apron. These parts aren't shown on the apron parts drawing for the 101.07403 but are for the 101.28900/28910.
2. The missing 10F-84 Knob is retained by a 3/32" x 1/2" Groove Pin,
3. Again, may not be original, but it retains the 10F-81 Bearing, part of the power cross feed.
4. Retains the 10F-17 Stud, also part of power cross feed.
5. On the back side of the apron, for one of the two alignment groove pins for the half nut guide. The only reason that I can think of for it to be drilled through from the front is that it was located off of the hole for the half nut actuator (scroll) shaft (which has to be drilled from the front), and then the other hole was located on the back side off of the first two. It's the same way on all of the 12" and 10"aprons or carriages.
6. Yes, a 1/4"-20 square head bolt which should be down in the hole and a threaded lock lever 9-42A.
7. That hole is for storing the 10D-260 oil or white lead dropper for when you are using a dead center in the tailstock ram.
8. for the square head bolt for the carriage lock.
9. Their purpose is to keep swarf (chips, shavings and dust) from getting into the cross feed screw bearing or onto the power cross feed gears. They are removed for oiling the bearing and gears, then put back in the holes and turned down flush with the top of the dovetail.
10. Yes, the screws are all wrong and yes, they should all have lock nuts.