At the risk of being somewhat repetitive, three methods that will work:
1. Salt and alcohol treatment. May fix the problems with the bowl, won't do anything for the stems. However, soaking the stem in Oxyclean may help. Then you will need to polish it.
2. GLP's "ghosts be gone treatment" is, IMHO more effective for the bowl. See above for stems.
3. What I would do: send my pipes to www.walkerpiperepair.com and let Mike solve the problem for you. His Ozone treatment will remove any trace of odor. Your pipe will smell like new--guaranteed. It's $5 for the first pipe and $2 for each additional pipe. If I get an estate pipe that's in totally disreputable condition, I send it to Mike and he sends it back completely sanitized, looking and smelling like new. Check out the prices for his various services. You won't have the use of your pipes for a few weeks, so you may need to pick up a couple of cobs at your local drugstore, but Mike's services always work.