I can't even imagine what might be in there. What kind of lab did you get it from? Inorganic or organic? Glassware that has been used exclusively for inorganic chem is generally easier to clean- just a good soak in fairly concentrated acid and rinse well with hot hot water. Anything from a lab doing work with pesticides, bio-chemicals, and other organic compounds MUST and I repeat MUST be baked off in a kiln before it can be considered safe.
Also yes if that is glue you are using to secure the stem, you should gently razor it out and replace it with a rubber one from the head shop.
If you must smoke out of labware, I'd follow these steps to make it at least a LITTLE less sketch using stuff you have around the house:
Scrub with hot hot hot soapy water, rinse.
Soak a week in white vinegar, rinse.
Soak a week in rubbing alcohol, rinse.
Run through the dishwasher.
Be safe and happy smokin'.