putting scales and things to use, and other questions

hey!
so there has been a couple obvious questions thumping around inside of my he
mainly for the topic of scales and things, i might ramble a bit so i'll rephrase all my questions i have at the very end aswell.
okay so i've been learning more scales as of recently, and currently i know the pentatonic major and minor in all five positions up and down the fretboard. earlier today i was trying to learn the five positions for the major scale aswell.
as it's the backbone of most music along with the minor. this was an attempt to escape the main major scale pattern
( the main one being E 1 3 5 )
A 1 3 5
D 2 3

now, this kind of , but not really brings me to my first question,
how do you know what to use for a scale when you've got a specific chord progression?
would you analyze the formula that creates that specific scale with what chords you're playing aswell?
for example lets use a basic blues scale formula
1,b3,4,#4,5,b7 and the key of C because it's so easy
if you were playing a 1 4 5 pattern ( C F G )
then it would fit wouldnt it?
and if you were really feeling spontanious you could play a Bb or a F# or an Eb aswell
this just covers major's and minor's but now is there any exception with playing an odd 7th , 9 th 13 th or whatever chord aswell?

now if you wanted to avoid chords completely and still and the same 1 4 5 flow or feel to it, as it progresses,
how could this be achieved? by incorporating target notes perhaps?
you could start a phrase or a lick on C and then progress it to F and have another phrase or a lick moving it onwards to G or back to C? could that be right?

continuing on, i've heard and seen many jazz guitarists play and flip through multiple scales and chords in a matter of minutes. say if it was the 2 5 1, ( yeah more cliche formula's ) D G C, could they flip through two or three scales while upon that chord if it goes back to the original D at the end, but play all of the scales in the key of C? or would they flip through say one phrase in the key of D using a certain scale, change to the key of G and do another phrase and so on with C?
or would it be a more ideal thing to target specific notes again within one scale depending on the underlying chord?

so, i'll mangle up a couple more questions later, but for now this is it
1) how do you know what to use for a scale when you've got a specific chord progression?
are their any exceptions? and how do you handle working with odd chords aswell like Cadd9 or Cdim7, do you analyze them as they are with the scales?

2) how can you incorporate and manipulate target notes within a phrase/lick/pattern to add flow or to be able to hear the underlying chord prog. without playing it ?

3) how would you play along with a chord progression with scales? this is the basics but would you use one scale or continuously change and go through many scales and continuously change the root note or the key throughout it ?

4) this is a stupid and obviously it changes from person to person sort of question but what could a mode or two i should work on learning? i'm more of a jazz player and besides trying to learn the 5 positions of the major scale to improvise upon what else should i invest into learning?

thanks for your time!