Theory and the roadblock

I moved this over from another forum where it wasn't gettng much attention. I'll include all responses. Please put your two cents wirth in.

My initial post, Ben---------
I am trying to move music theory into practice. I have the modes of the major scale under my belt, I know which are major, minor, etc. I have memorized each note as a major interval, minor interval, flat diminished etc., for instance.
Ionian M1 M2 M3 P4 P5 M6 M7 tensions 9 11 13 avoid 11
Lydian M1 M2 M3 #4 P5 M6 M7 tensions 9 #11 13 avoid none

I know for instance that the Dorian mode starts on the second note of the major scale and that each subsequent mode starts on successive notes of the major scale. I know where the root and fifth relative to the patterns, as long as I am playing modes/patterns of the Major scale. Here is my problem. Lets say I am trying to solo over a major cord progression with a tonal center of A and I want to use A-Lydian to tweak the mood. I just hit a brick wall in trying to apply root, fifths and tensions etc. because when I changed from A-Ionian to A-Lydian all special notes moved relative to the patterns of the major scale I have memorized. How do I get past this roadblock? What mental approach do I take to make this less complicated.
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I got nothing of value then I later added the following

Perhaps I was unclear or just don't understand. I play A-Lydian the same as others by placing the root of the pattern on the tonic A in this case. I also know the position of all notes in the scale by applying the normal patterns. The problem I am having is locating specific notes of the scale within the pattern. For instance where is the #4 of the Lydian pattern when playing A-Lydian? Where are the tension notes 9, #11 and 13? Suppose I move to the Phrygian pattern of the A-Lydian scale. Then where is the #4 of the Lydian scale? Where are the tension notes 9, #11 and 13?

If I stop and take a minute or so I can always figure out where the special notes are, but that doesn't work while jamming. It becomes even more difficult if you switch scales every few bars. For instance, playing Blues in A it is common to play A ionian or A minor pentatonic over the I chord, A-Dorian over the IV chord and A-Mixolydian+Blue notes over the V chord. At least in Blues this is repetitive because the chord sequence is very repetitive.

I understand that in country music it is common to change scales with each chord change. So how do you quickly identify where the important notes are?
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After several posts I was left with the following two options.
1) Just use my ear and experience. I am sure this works, but lost of experience is needed, and you get the occasional "Ooops".
2) Memorize the notes of all the scales in all keys including the tension notes. A lot of work to memorize and easy to forget.
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Please let me know how you address this issue?