Hi richardw.
I've read and reread your post and I find it a bit difficult to follow, but I do get an idea of what you're asking.
Chords are built from one scale, the key scale. So if we're talking about E, all 7 chords that are in the key of E will come from that one scale, using the simple formula of selection that is on page
http://www.guitarforbeginners.com/chords.html
The E scale is:
E F# G# A B C# D# E
In E, the V chord (Five Chord) is B7. It comes from the E major scale. Its notes are B D# F#. A four-note chord requires that you add the next candidate to the triad. That note will be 'A', again, following the formula.
In the context of B, though, A is not the real 7. The 'real' 7 of B is A#. So the chord must be named B7, not Bmajor7.
In the context of the key of E, the B chord's scale is the Mixolydian Mode. In other words, starting and ending the E scale at B, you wind up with another scale; it's identical to the mother scale except that the 7 is flat. So, instead of:
T T st T T T st (the major scale), you get
T T st T T st T.
THAT'S where the flat seven comes from.
That descibes one mode, the V chord mode, the Mixolydian mode. It's just the major scale's intervals starting at a different root. There are 7 modes, naturally.
My advice is to get an understanding of what modes are, but don't get hung up on them. They tend to take care of themselves as long as you're aware of the 'mother scale', the I chord's scale.
I hope this helps a bit.