Ok just tuned down to A standard. A D G C E A. G and C are in tune, sound great. E and A are in tune sound great. But C and E are NOT i. Tune sound bad. Why?

Are you using an appropriate gauge of strings, and are your intonation and action set up properly?

Yes. 13-73.ow action. Intinatio. Is good on all strings

Well, by the sounds of it, you're tuning strings relative to each other, or at least testing them that way. But G and C can be in tune relative to each other AND E and A can, but each pair can be out of tune relative to the other. So, you should, for example, get C in tune with G, then get E in tune with C, then adjust A to be in tune with C. Just go down by adjacent strings one at a time, then play some chords to test the bunch together...

are you sure about the intonation? is your C string wound or solid?
you probably already know since said the intonation was good, hook up your tuner to your guitar. the harmonic at the 12th fret and the fretted note at 12 should be identical. if not, adjust your bridge in or out depending on whether it is sharp or flat.

if the intonation is all good, there must be some other defect. is the neck is straight, no twist, thicker strings sitting in the nut okay, bridge height is good, etc.?

Besides using the proper gauge, did you have it set up to handle the heavier strings?

Is it staying in tune or just doesn't sound good in the first place? The winding might be slipping .. ?
Maybe use a digital tuner and just go one at a time instead of relative?

It would help to know if the strings are in tune when you play harmonics.