Vapor Barrier for Wine Cellar

No, you only want a single vapor barrier. A second vapor barrier would create a moisture trap that would cause more mold issues. If there's a condensation issue, I'd replace the section of HVAC ducts with an insulated duct. The insulation inside the duct prevents the outside metal part of the duct from getting cold enough to result in condensation.

Yep, the 120 year old houses do make life more interesting (and expensive and/or colder.)

Use an air barrier that is NOT a vapor barrier. More commonly known as housewrap. Vapor moves through, but bulk air movement is reduced.

For insulating inside the floor joists, either blown-in cellulose (which supposedly has very little issue with vapor, due to having very little air movement through it) or a sprayed foam product. Getting good fill blind (without blowing out the ceiling, in the case of the spray foam) is tricky.

I presume you don't want to rip out the ceiling for better access - but you really need to think hard about getting some drywall below the XPS (or XPS and added air barrier), or you have (and have now) a major fire hazard - plastic materials exposed in a garage that's below occupied space. The plaster ceiling above it may not burn through for a good long time, but the smoke from it will do you in even if the structure is unaffected by by a fire.