Mike,
I had a similar experience when I replaced the slave. I used the same long stroke cylinder you did and found it a little loose in the bracket. The loose fit doesn't particularly matter, I suspect if you wanted to paint the bracket the cylinder would still fit. I plated mine because I didn't realize the extra clearance.
The same black fluid also came out when I drained the system so I just kept adding and purging until I got clear fluid. I did not have any problem with air trapped in the system either. I also ordered the flexible stainless line that Pantera East has that replaces the scary clampless plastic line that is original equipment.
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