Quarterly Pipe Cleaning

I dip a pipe cleaner in to the bottle and go to work... pretty soaked down 2 or 3 inches and i never had a problem. I use 80 proof whiskey and it works just fine.

I'll take a pipe from the rack for the day, smoke three or four bowls. After each smoke I'll use a dry cleaner, front and back, to clean the airway. Before I rack up the pipe, following its last use, I'll dip a cleaner in ISO, clean the air way, repeat with the other end, bend in half and clean the chamber. Disassemble, and swab the mortise and plenum on ocassion. Then, a small piece of paper towel to clean the rim, and wipe down the pipe and stem. Olive oil every now and then. I find if I do this, I never have to thoroughly clean my pipes.

Smoker
You mentioned that you clean the pipes quarterly. But how much do you smoke each pipe?
Some on the forum have mentioned that they do a full clean after 10 -15 bowls. That may be the amount you smoke each pipe per that time period, but maybe you smoke them much more than that?
I just had a Dunhill that was smoking bitter for me and I decided after general cleaning did not work, a salt and alcohol treatment was necessary; if that didn't work, I was prepared to do a retort on the pipe.
No big deal, but I believe in not removing the stem from the pipe a buildup of tar can form between the tenon and the shank, or, the inside section where the stem fits in. I just read on Mr. Roush's website that he does not recommend taking the stem off the pipe for frequent cleaning after a smoke; I'm not sure that I agree because the buildup is definitely there.
You did not mention that you use a pipe brush. Maybe you should consider that in your general cleaning. Pipe brushes are available at most of the suppliers.
Good luck

When I finish smoking a pipe (briar) for the day (1 to 4 bowls) I pass a cleaner through it and leave a second in the pipe then return it to its storage place. The cleaner in the pipe tells me on Sunday which pipes have been smoked the previous week. These pipes will get a soaked cleaner through them, possibly a wire cleaner if needed, cake checked and maybe a bit of reaming. The bit gets a wipe down and the pipe is returned to the rack ready for another use.
I pay virtually no attention to the exterior of a pipe, a little oil of the nose now and then when smoking and a buffing with a cotton handkerchief when the pipe is returned to the rack.

I follow most of what kashmir wrote. Probably got it from a prior post of his anyway. Since I smoke arro's I also dip my folded pipe cleaner in cleaning fluid. I also pat dry the bowl after cleaning with a paper towel or cotton swab. Although I have gotten good at smoking it to a decent ash, it still gets a wet spot from time to time that I hear will build up a bad taste if left uncleaned. In addition to running pipe cleaner after each smoke I also do it when it gurgles to soak up the wet. I smoke at least 4-5 bowls a day sometimes leaving half in the bowl for my next break.
*** When my pipes taste funny though and if its cool I take it apart and suck some air through both the stem and the back of the bowl. This tells me where the taste is coming from. Most times for me it has been the stem. I go from there.

The only time my pipe gets sour is if I puff too fast and/or too hard. Usually happens when I smoke Latakias.

Whenever someone says "bitter" I wonder if it is really a pipe gone sour or if it is oxidation of the stems. Remove the stem see if you get the bitter taste with just the stem. If so, no amount of alchohol or pipe sweetner will help. You will need to clean the oxidation from the stem.

Here's what I do for a deep cleaning;

1) take the pipe apart

2) ream the pipe if necessary

3) using whatever alcohol you prefer, dip a shank brush in the alcohol and scrub the shank and draft hole vigorously as much as you feel is needed

4) using pipe cleaners bent in a "U" shape, dipped in alcohol, twist them into the bowl

5) dip pipe cleaners in alcohol and run through the shank and draft until they come out looking the same as when they went in

6) run a couple of dry fluffy pipe cleaners through the shank and draft

7) run a alcohol dipped cleaners through the stem until clean

8) run a couple of dry cleaners through the stem

9) if necessary, de oxidize the stem using your preferred method

10) polish/buff the bowl using you preferred method

11) put the pipe back together, insert a pipe cleaner from stem to bowl, rest the pipe upright with the bowl down and let it sit for 24-48 hrs before smoking

Just a couple of thoughts. The cleaning routines listed above are all excellent and should keep one's pipes from going sour, provided that the pipes are in good condition to begin with. With respect to Mr. Roush's caveat, I always take apart my pipes for final cleaning so that I can remove any deposits from the mortise. I haven't experienced any consequent problems with the fit between the stem and shank. At the end of a cleaning the airway is thoroughly clean, no oily deposit to become rancid. The pipe rests for at least a week between days of use.

Even with a careful regimen, some pipes will still get a bit acrid from long regular use. If that happens, they can benefit from a long period of rest, anywhere from a few weeks to a year. Consider the addition of a few cobs to extend your rotation while your favorites get an extended rest after a thorough cleaning.

The other factor to consider is your choice of tobacco. If you are experiencing irritation it might be helpful to change what you're smoking. Virginia bright hits my mouth like battery acid. Even the smallest amount stings, so I completely avoid it. Your choice of tobacco might be contributing to the sour taste of your pipes.

I remove the stems after ever bowlful ... only after the pipe has cooled for hours, though ... I clean the stem, and shank with a bristled cleaner, fold the cleaner and brush the mortise, then use it to brush the interior of the bowl ... I repeat the process with a bristled cleaner if the first pass found more than the usual amount of 'gunk' ... then I repeat the process with a fluffy cleaner and repeat again IF the cleaner comes out with more than traces of 'gunk' ...
About once a month I dip both bristled and fluffy cleaners in 151, then repeat as needed for the pipe cleaners to come out virtually clean, then follow with a dry fluffy ...
My pipes are always completely clean when I pack and light them ... if I decide on a second bowlful, I use a second pipe ... overly anal? ... maybe ... but in early years, I used to smoke my pipes repeatedly throughout the day and do a cursory cleaning at best between bowls and a less than rigorous cleaning at the end of the day ... I've learned that there's a lot of difference in the smoking experience that comes from a clean pipe ... enough so that I'm willing to put in the relatively small effort it takes to keep mine that way ...
I don't judge those who're doing it another way ... if they're happy with their experience, that's fine with me.

Kashmir,

Doesn't the olive oil get sticky?

I used olive oil for a brief period, doesn't get sticky. Buff it off with a paper towel or cotton cloth and you're good to go.
Wax is probably the better path to take but this is the poor man's solution, and I thought it worked beautifully. You're going to be touching the pipe and stem so much that you'll slowly take away the oils back from the pipe. I've never had a pipe go sour or become rancid because of olive oil use.
That's not to say go crazy with olive oil, use it very sparingly. It's food, not pipe polish. At the end of the day you eat olive oil.
There are so many other options, but it's not going to hurt anything as long as you use common sense and clean the pipe like you should.
Getting back on topic...
@smokertruck
Are you letting the pipes rest for a few days before you get back into smoking them? Changed tobaccos? Maybe it's the blend that has changed and not the pipe that has soured?
If changing tobaccos doesn't help then try shoving some cotton balls in the bowl and shove some Q-tips or something in the shank to prevent it from spewing out the other end, and then pour some of the alcohol you use to clean it with. I wouldn't recommend using iso alcohol for the soak, find a vodka or rum or whatever.
Check on it every now and again and top it off and let it really soak in that delicious libation.
After a few hours pour out the pipe and remove the cotton balls, you may choose to repeat this process or let it dry for a few days and then smoke it to see if she's cured.
Rinse repeat if it didn't work.