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Black spots on Swords & Reference books advice needed

I am fairly new to aquatic plants (3 months) and been lurking on this
list for a while and slowly learning, however I would like to ask some
questions that may be awfully basic so please bear with me.  Thanks for
any and all comments and suggestions.

I have a 29 gal fw tropical tank with about 15 plants in it.  My 3
amazon swords each have a few leaves that have developed small black
spots on them.  They do not rub off like an algae would.  The water is
very clear, 0 ammonia and nitrites and pH 7.2 to 7.4. Temp is very
constant at 78 F.  I have 3 ottos which keep all the algae out, hardly
any algae visible. The plants generally are growing well.  The tank has
a 20 watt fluorescent and it also gets afternoon sun from about 10 to 15
feet away.  I have big windows facing directly West which give lots of

 Is this a nutrient deficiency? An illness? or something else.  I use
Tetra FloraPride with water changes and have an UGF. I also use aquarium
salt 1 tbsp per 5 ga.  Also have lift tube with carbon filter on it.

2 of these plants also have sent up a long stem with one leaf on it to
the surface.  Should these long stems be trimmed.  

Does anyone have suggestion for a good reference manual for aquatic
plants in fw tanks?  I would like reference that has pictures for
identification, descriptions ideal conditions, and rating of difficulty
to grow, plus having basic plant care etc.?

I have searched both amazon.com and barnes and noble but the
descriptions are not clear enough to decide which would be good
reference sight unseen.