You can get very close to the 100 hrs if you drag the game out like I did and do everything.

The runners don't bring you malachite gems, they bring you ore.

here are a few of the gems I know about off the top of my head

In the horror of high hall quest you get 2-4 gems from beatrice from completing it, there are some traders you can buy them from. Also, look for Malachite ore veins and save before you open them so you can reload if they don't give you a gem.


I am sure I missed a bunch so others will have to help now