Hi Chops,
Different folks have different methods of cleaning up an estate pipe. Here's what I do:
Remove the stem from the shank (a tip: twist the bit in the same direction; not back and forth. You're less likely to put strain on the shank if you go in the same direction).
Sit the bowl in a pipe rest so it's upright (not tilted too far forward). Pour a small amount of high proof neutral alcohol (grain alcohol or vodka)into the bowl. Stop before it pours out the bowl or the shank. Let it sit for 10 or 15 mins. Another option besides alcohol is the little green bottles of "Pipe Sweetener" they sell in pipe shops (I'm pretty sure some of our sponsors sell this as well). It's pretty much just alcohol with coloring and scent added.
Pour out the alcohol. Use pipe cleaners to clean out the shank until it is no longer gunky. I prefer using the bristle type, but it's your preference. If the shank is wide enough, you could even use Q-tips. If the bowl cake is acceptable, I'd take a thick, fluffy pipe cleaner, fold it in half, and rub it around the inside of the bowl, again until it's no longer gunky. Let the bowl sit for at least 24 hrs and repeat the process.
As for the stem, again it depends on how gunky it (inside and out). If the outside is shiney, I'd use a LOT of pipe cleaners and alcohol and swab it down until it's clean. Let it dry. If the outside is oxidized/gunky, I first use a SMALL amount of Brasso cleaner and a toothbrush to scrub it, followed by regular toothpaste and a different toothbrush. I've also read of people using Mr. Clean Magic Erasers with good results, but so far haven't tried that myself. Depending on how shiney I want it, I may lightly buff it (my local B&M has a buffing wheel) then coat it with some Obsidian pipe stem oil.
Again, different folks use different methods. Let us know how it goes.