Fix output; some was breaking --json, some typos

[pvdz]

Some minor output fixes

• various cases of logging to stdout that was breaking --json, temporarily doing an .error() but we'll change the logger soon to always output non-log commands to stderr and then we can do a sweep through the .error() calls to see what needs to be different.
• Some textual changes and fixed some missing parenthesis in text (the bot caught one the other day but apparently didn't think it was important for the others)