I am happy to hear that there is so much interest in a new user guide. In the mean time, the Diallo workflow is a good place to start. I am expanding on and simplifying the process of setting ink limits, defining cross-over points, and easily linearization.
Like others have mentioned, photospectometers like the i1 used in measuring ink density and test charts are different than those used in other applications in that they emit a specific wavelength of light and measure the reflected values at various wavelengths. The software takes that data and uses internal formulas to translate it into CIE Lab or CIExyz values. Those values can then be translated into density with a different formulas. I don't worry about the math; that is software is for ("damn it, jim. I'm an artist, not a color scientist).
I think a used i1 can be one of the most valuable tools for creating QTR curves because it allows you to quickly, accurately, and consistently record the densities. Those data can then be copied and pasted into spreadsheets to evaluate density or used with the linearization tools within QTR (as well as to create ICC profiles for softproofing). I think the scanner and photoshop script workflows are useful when one doesn't have access to a photospectometer, but those tools/workflows can be inconsistent, and the QTR curve tool is dependent on comparing to known values to work with linearization. I am considering making prints of 21-step charts that include the Lab measurements for people to use as a reference for the QTR Curve Tool photoshop script.
Linearization seems to be the main issue for people, so I will try to give some attention to the subject in the future. The QTR tools are very good at doing the linearization job without the need for spreadsheet transfer functions or phootshop .acv curves. QTR allows you simply measure the values, either density or L*, and enter them in the descriptor file. The linearization correction curve is created automatically though the install script on the Mac or when you save the profile in the QTRgui for the PC. Because I started making curves/profiles as a text file on a mac I still prefer to do it that way on the PC. I just open the .txt file in the QTRqui and save it to create the .quad file.