I think I may have answered my own question, I did a more thorough search of the Cozy archives and found a post from Doug Shepherd. He believed the contamination was from assembly grease but it never caused a problem.
Date: Feb 27, 2000 5:32 PM
From: Doug Shepherd <DougSheph@home.com>
Subject: COZY: Stuff in epoxy/Michael Engineering pump
I'm also using the MGS 285 epoxy, and the Michael Engineering variable epoxy
pump. I also noticed some minor traces of contamination when the pump was
new; the instructions said that this was a lubricant used to grease the
seals and the small amounts that get into the epoxy won't cause any
problems. I've been using the pump for a year now and notice the black
stuff only occasionally now. The pump doesn't leak, bind or otherwise
misbehave (as long as I use it frequently enough to keep it limber, anyhow),
and I've never rebuilt it or had to replace any of the seals, so I wouldn't
worry about the seals deteriorating.
I love my Michael Engineering pump, and I recommend it highly, but I have
one word of warning about it: be careful not to put any sideways pressure on
the reservoirs, either when you're filling it or when you shut the door of
your oven. They're not supported very well and they crack easily, as I
found out the hard way. That resin's expensive, and there's no point
wasting it on the floor of the garage.
Doug Shepherd