In addition to what jeff101 mentions, there is now print protein 3.0 which fixes problems with chain detection and makes some other more minor improvements.
There are a couple of spots in print protein where you can copy from a dialog, then paste into a speadsheet. (They are tables in CSV format with the tab character as the delimiter.) The first and most important one is the "Subscore Report", which gives you all the subscores for each segment in the puzzle. Position the cursor the in the "subscores" box, then control + a to select all and control + c to copy. The result can be pasted into Excel or Google Sheets or the spreadsheet of your choice.
You'll probably be able to see only the "end of report" line in the text box, but the whole thing is in there.
For electron density puzzles, there's also a "Density Report" dialog, which has two separate outputs that can be copied and pasted. The first is the "density analysis report", which gives some density statistics. The second output is "density deviation" which is just a single line, one character per segment, with a plus, minus, or equal, indicating whether a given segment is above, below, or equal to the average density. For larger puzzles, the version of density deviation that appears in the scriptlog will be more readable, since it has rulers indicating the segment numbers.
All the copy-and-paste reports and some additional items are present in the scriptlog file. Despite the XML extension, it's mainly a text file.
Also, the scriptlog file is named after the current track, so "scriptlog.default.xml" just means you're in the default track. The tracks dialog can be found in the undo menu. I've assigned the hotkey alt + t to open the tracks dialog. I now use tracks much more often than I used to.
You can contigure hotkeys in General Options (control + t), on the Controls tab, under "Configure Keyboard Shortcuts". If you scroll down carefully, you'll find "General: Tracks", right after "General: Show Residue Information". For Tracks, click on the hotkey box to the right, which is blank by default. You can then select the hotkey of your choice just by typing it.
Tracks are handy in cases like the small molecule design puzzles, since the current score becomes the credit best score. So if you have one small molecule that's gone as far as you can get it to go, you can load a new small molecule, then create a new track. The new track will only know about your new molecule. Restore credit best will be the best of the new molecule. Back on the old track, credit best is the best of the old molecule.
As far as copying from the recipe output window, it's a line at a time as you noted. That will probably never change. Also, the recipe output window is not resizable, and you can't change the font or font size. Again, I think we are stuck with that, despite suggestions that were made long ago.
