how can I get the crud out of my plumbing

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.