Whoa!
The engine on my DT400B was seized up when I got it. The flywheel was rusted and became attached to the lower portion of the side case. But it was no where near as rusty as yours. You win!

imgur.com/a/1c6m3F3

That looks nasty, were you able to get it cleaned up? It is hard to believe it was running like that.

Got the double shoulder screws and wonder if they'll work...anyone know? The bottom pic is the same as was in the clutch

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That’s interesting because I just disassembled two JT clutches and one had the double shoulder screws and the other had the typical shoulder screws. I have no idea why they are different between the two clutch assemblies but they both worked fine.

imgur.com/a/O9ZttdF

They will work on the DT360 clutch but will be weaker if disengagement exceeds the clutch boss length and the pressure plate may no longer align w/the grooves under normal movement. If the length of the screws are shorter/longer, expect a different pressure on the plates.

The screws compress springs for pressure and in the event you disengage the clutch far enough become an extended part of the clutch boss. So, if the pressure plate extends that far on a disengagement, it will twist out of place place from the clutch boss intended alignment. The twisting movement will be applied to a smaller diameter of the screw at this time IF the thickness of the pressure plate is less than the length of the screw where it is reduced in diameter.

The following is a picture of the plate engaged and disengaged. You can see w/7 plates the clutch gets no where near the end of the boss, ie so your screws ~should be safe. : ) If you add a ball to the pushrod and go for 8 friction plates, something different may occur.

This pic illustrates the plate on the boss even at full disengagement.

As long as the total shoulder height is the same, should be fine.  

No worries about strength on the stock clutch with the toothed pressure plate.  (If you tried to modify and add more discs, cover probably wouldn't fit.  Yamaha was very conscious of case width in that era.)

Either of those screw designs just need to be snugged tight though...  what tends to break them is overtightening.   Also be sure to use the correct tool to hold the inner basket while tightening nut.  Never try to use a screwdriver or something against the outer basket (or on the inner basket screw bosses) to hold the inner basket unless you want to break parts. 

(Don't ask me how I know)