I don't think alcohol is a conscience matter. I think they're pretty clear on the guidance: it's okay to drink alcohol. It's not okay to get drunk.
Now, smoking is a firm no, as far as I understand.
I thought that there was a time when some of the blood issues were left to the individual's conscience? Not full blood transfusions, but fractions, like for hemophiliacs?
In CoC, Ray Franz mentioned the issues they had with trying to regulate intimacy for married couples. It became such a mess that they finally just relegated it to a conscience matter.