A rock with a porphyritic texture is cross cut by a stockwork of quartz veins. Bordering the veins is extensive alteration of the host rock. The vein contains fine-grained (~1mm) chalcopyrite and molybdenite.

I believe it to be a hydrothermal ore deposit as porphyry ore formation, stockwork and the Cu-Mo-Au element list indicates.

Is this a correct line of thinking and if so is it specific enough, do you think?

What happens is that there is a magmatic intrusion (the porphyry), which then solidifies. When it solidifies, it expels acidic hydrothermal fluids which carry metals in them - most often copper (represented by chalcopyrite) but also sometimes molybdenum (represented by molybdenite).

Once the fluids hit solid rocks, they react with it, and become neutralised. The carrying capacity of the fluids diminish, and they deposit the metals into the minerals you observe. The solid rocks can be pretty much anything. It can be the porphyry itself, another porphyry that happened to be around, sedimentary rocks, or whatever.