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As far as joint/axis being uncoupled that is possible with the newer version of LNC you may only need joint mode. However, for position mode still active I don't see it anywhere in the hal files you have posted. 

There is this line in your configuration, which I don't know what it does 

net motion-in-position motion.in-position => vc-p1as.is-moving.

This line uses motion.in=position from the motion component not halui. so you have a mix of halui component and motion component for jogging I wonder why they choose this complicated route. I am going to the gym now I will have look at your hal files later and report back.

When I boot the computer, lspci -v shows the card, and i can jog the stepper. But after a little bit the stepper stops working and lspci -v shows "(disabled)" next to the ports. The only way I've found to get it working again is to reboot.

I have the windows driver installed (dual boot), do you think that could mess it up on linux somehow? It's just weird that it works and then becomes disabled partway through working, so i figured maybe that patch would help. Unless the patch is outdated and the latest kernel already supports 9900?

Also, when the stepper does jog, it will stop for a split second intermittently, and then soon after show "joint 0 following error". It also shows "unexpected realtime delay on task 0 with period 100000... run latency test and resolve before continuing," I already ran the latency test.