I'm still pretty green on how this works as well, and finding/marking all the items, incl even the first one, the clockwork assmy.
First of all, there's no marking needed.
The Assembly drops into your backpack when you start the quest.
To start collecting items, you click on teh assembly and choose yes.
ALL of the items are IN THE AREA AROUND SUTEK'S HOUSE, which is why it sucks when he's not where he's supposed to be.
You just run around the inside of his house, and around the outside for a few of the items (the stone types, barrel hoops, barrel staves, thorns, etc.) clicking the items and running to the next one like a madman. note that not everything looks like the standard version of the item asked for (the way the boards are stacked, the use of the deco ingot stacks that look like the Minor artifact gold bricks, vases for the powder, beakers/flasks as the potions, etc.).
Just walk around his house, inside & out, mousing over everything, to get an idea where everything is, before starting.