I can help with a few:
Red bar beneath a glyph in the font window means it's the master glyph in a kerning class.
Navy glyphs in the Metrics window are non-master glyphs of a kerning class.
Red kerning pairs are defined exceptions in class kerning.
You should read the Class Kerning section of the manual, which covers all this comprehensively.
I myself haven't figured out under what circumstance a hinting symbol is displayed under a glyph in the font window. Sometimes they're green, sometimes red. They only appear if there are overlapping hints, but I haven't yet figured out the colours.
I should probably re-read the Hinting section of the manual I guess!