My house was built in 2000 and has a well. The previous owner didn't
have any type of filter on the water and there was a hydrogen sulfide
problem that I eliminated with the install of a backflushing pyrolox
whole house filter. Water quality is fine now and no issues.

My problem is that whenever I shut down (only a few times) the water
and drain the system (faucet valve repair, moving pipes for
remodeling) and then start the water back up, I get this black stuff
coming out of all the faucets for a few moments...it almost seems like
a grease of some sort. Well I just had to relocate some pipes and I
notice that the insides of them are coated with this stuff...not a
large buildup, but the entire interior of the copper pipe has this on
it. I have noticed this everytime I cut into the plumbing. I am
assuming it is from the pre-filter days. Anybody know how to get rid
of this stuff?

I had to do this in my ex-house. I had galvanized pipes and high iron/
mineral content. The insides of the pipes were darn near shutoff from
grit, scale etc.

Buy a shop vac if you don't have one and set it up for water pick up,
ie, remove the paper filter and leave the sponge filter on it.

Go the fixture furthest from the entry point of the water pipe into
the house and remove the water valve from the pipe. You can do this by
unscrewing the packing gland nut and occasionally unscrewing/opening
the handle. The valve will come out.

Setup the vacuum at this location. Now go shut the water off at the
main valve where it comes into the house. Then open the faucet in
another bathroom or kitchen and suck the water out of the pipe where
you took the valve off. The air bubbling through the water will clean
the sides of the pipe.

An easier way would be to use an air compressor. Take a short piece of
garden hose and adapt the one end for connecting to the air compressor
and the other end screws onto an outside faucet. Pressurize the garden
hose with air pressure above the highest water pressure the well pump
will put out. Open the outside faucet, take the aerators off all the
sink faucets and slowly open the faucets one at a time and the air
will go in the pipe and come out the other end you have open, along
with water spurting and black crap and whatever else is in the pipe.
After that one runs clear, do the other, hot/cold. Do this for every
faucet in the house. Then take your shower heads off and do the same
thing opening each one one at a time. I'd limit the air compressor to
80 psi just to be safe because you don't want to over pressurize the
water heater.

Those air bubbles will really work, you'll be amazed.