Oh, the crap people put themselves through in the pursuit of trying to do it right. I've heard the "never take off the stem" nonsense. I think that it's a ploy by pipe makers to cause their sold stock to develop foul mortises and sinking sour flavors so that the stink will force the pipe's owners to buy replacement pipes.
Some pipe carvers, such as Jim Cooke, have said that the stem should never be removed. But this is meant to deter those who would remove the stem after EVERY bowl, as constant removal could lead to problems by placing excess stress on the shank. After all, if the stem was never meant to be removed then why did Dunhill place a dot on the stem to indicate which side is up?
I'll run a pipe cleaner or two through the airway between bowls if I'm having more than one in a day. But I'll remove the stem and clean out the airway and mortise at the end of a days use. I'll use tapered bristle pipe cleaners to scrub out the shank airway and mortise and fluffies to soak up moisture. For the mortise, I'll fold up a pipe cleaner enough to make for a firm fit and swab out the mortise. For the stem, I'll use fluffies and/or bristles which have been dipped in isopropyl alcohol to remove gunk. When the pipe cleaners come out substantially clean, I'm done with cleaning the shank and stem.
Unless I'm getting some sort of ghosting, or I'm cleaning up an estate for the first time, I avoid using alcohol in the shank as it's not good for briar. Exposure of briar to alcohol needs to be kept to a minimum since alcohol leaches out mineral soluables in the briar that contribute to both it's heat resistance and its moisture absorption. Overindulgence in cleaning with alcohol can gradually reduce a pipe to a hot wet smoker.
The chamber gets cleaned out with a folded pipe cleaner or two, dragged over the walls to remove loose tobacco particulates and dottle, and is next wiped with a paper towel.
As soon as I've cleaned out the airway I reassemble the pipe and put it away to rest for a week or longer.