No problem. Right now, the yellow position has the lightest dilution of the Eboni-6 ink. The .qidf profile I've made tells QTR to only use the 5 ink positions, and do nothing with the yellow ink position. That's done with setting the number of gray parts to 5, and not specifying anything for the yellow position. You can also specify that yellow is an unused ink, though QTR is smart enough to figure that out on its own if you don't say anything about the yellow position. I believe mechanically, the printer expects that position to be fitted with a non-empty cartridge, otherwise the printer will not work, and I think that's what Paul R. meant.
When I add a toner, it will be added to the toner_1 settings, and I'll specify that the yellow position holds the toner, and how much of it to use. I ordered the Canon inks from Atlex as well as additional carts and bottles from MIS --- we'll see how quickly they deliver ...
I do use a spectrophotometer: it's the ColorMunki Photo, which I think is the cheapest available one from a major manufacturer. The QTR linearize app can directly parse the CSV output of XRite's ColorPicker app, so after I save out the 21-step scan, I just drag the .csv file on top of the linearize app, and it produces the file for me. Keith Cooper of Northlight has a ColorMunki-compatible 21-step wedge that I use for my linearizing scans.
I actually use Richard Boutwell's bwmastery.com Excel spreadsheet (it works fine in Apple's Numbers) to do my linearization as it's a bit more forgiving than QTR's and shows you more information too. This spreadsheet parses the output of the QTR linearize app.
It is pretty complicated even with a restricted paper set, but after a while, you kind of figure out an efficient workflow so it's not so bad. For example, I've made my own version of an interpolating spreadsheet to facilitate finding the ink crossover points. It still involves a bit of manual copying and pasting, but it's helped me do that part of the process in a relatively error-free way quickly.
On the paper front, I have some Canson Rag Photographique 310gms now, and it appears to have a slightly warmer white point than the 210gms version. That helps with making the inks look more neutral. I just relinearized for that paper, and kept the crossovers the same.
I also have some Awagami Kozo Thin Natural coming to test out. I'm very curious about Japanese Kozo paper, and this is a relatively cheap way to try it out. Ultimately, I'd like to try their Bizan paper, but it's way too expensive to try on a whim right now.
Good luck with your own printing! I'm always happy to help.
--Andre