Ok, so I think I have solved things, and figured it would be good internet etiquette to respond to all this here in case someone else has a similar issue and finds this thread via google or something.
I took the slave off again, and yes the shaft was free to move inside. I think the issue was with the slave cylinder afterall. It was more or less at its maximum extension. I pushed the piston back in and out a few times and realized it had been at max extension earlier. While I was working on something else, the slave piston ended up pushing itself all the way out so I needed to re-bleed the whole system, but we're in good shape now.
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