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Tranny issue
I'll venture that your obstacle has nothing to do with using headless bolts as guide pins; I have seen, and used, that technique several times.
I would predict that your clutch disc is not precisely centered on the axis of the pilot bearing in the flywheel, so that even though you get the transmission input shaft splines to go into those of the clutch disc, as the tip of the input shaft reaches the pilot bearing if it is off even a fraction of a millimeter it will not go into the pilot bearing inner race. Check the centering of your clutch disc again. To do so does not require removing the clutch pressure plate from the flywheel; just loosen its bolts around its periphery, evenly, until you can slide the clutch disc around using your pilot tool so that the disc is precisely centered.
Another, less difficult issue, might be that the splines of the input shaft are not aligned with those of the clutch disc. With the transmission teetering on the jack, it would be easier to rotate the engine's flywheel a few degrees by levering it with a screwdriver against one of your 'installation studs'.
Good luck with your project!
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