I'm currently doing the prospecting missions but am unable to use the Mk II's scanner to register the ore as "found". With the configuration of the Mk II as 3 large ports, this prevents you from using the provided small port scanner.

This isn't a bug, the scanner is built into the MkII. Try a hog II with a adv scanner and a some type of large port beam. It will go a hell of a lot quicker.

yeah.. the prospecting missions are alot of space to cover.. and if you're just prospecting you wouldnt even need a mining beam, just something to carry an advanced mineral scanner around at a high rate of giddy-up (u'd needa get one off someone who already has done all 120 missions, but the 750m scanner on a fast ship (like the infinite turbo hog2) is a good prospecting setup

I could have sworn i've done prospecting missions with the integrated scanner on a Warthog Mineral Extractor...