So the New Reproduction clutch comes with new studs, but the stud has a shoulder on one side..which side goes into the clutch and which side sticks out that you can see..BTW the hardware washers are Wrong...shoulder pictured stud is on the right...

Looks more like a "pilot" to me, makes it easier to spin a nut on.
Towards the engine, I'd say.
I'd also want full engagement into the fan clutch.
(Neither of my BBs have clutch fans to compare to)

This is my 2863263 fan fluid drive unit that was a parts department replacement date coded 7/30/73 ("G30DB") for my '69 Barracuda 340 w factory air. Photos taken before it was rebuilt.

The stud was stuck tight, so I left it as (maybe) the Eaton factory installed it. Note the polychrome green inspection mark at bottom of first photo.

The unit was rebuilt for $300 in 2012 by:

Vincent Catalano
Pampered Corvettes
1396 East Main Rd.
Portsmouth, RI 02871
info@pamperedcorvettes.com

Not sure if he is still in business, but he was quite knowledgeable about Eaton's markings and date coding. He said this exact Eaton unit was also used on Fords.

The fasteners I found on my car:

4 - all thread studs 5/16-24 x 1", same machine screw point each end, phosphated.
4 - hex nuts 5/16-24 x 0.27 thk, 1/2 AF, Gr 5, clear zinc plated
4 - 5/16 conical washers 0.33 ID x 0.62 OD x 0.08 thk, phosphated

These photos are after the rebuild, and the restorer's phosphated studs and zinc plated nuts are about the same as I found, but the washers are incorrect. The nuts do show Gr 5 marks. Note that the flanged shaft is phosphated. According to the restorer, the new markings are also correct, because, he said, Eaton had several formats for marking. I asked him to change the date code for appropriate to my car's build date of about mid November 1968, maybe September 10.