I forgot to say, I used HALF POWER Mod.
http://www.ceriatone.com/images/mods/JCM800_2204CeriatoneHalfPow.jpg
I discovered that this mod schematic is different from "Two-EL34-Half-Power mod" in general mods section.
http://www.ceriatone.com/images/mods/Two-EL34-Half-Power.jpg
I revert back to original schematic without mod but I see that, there is no phase difference between LO input and speaker output but there is 180 degree phase difference between HI input and speaker output.
May be this is the case with half power mod, I did not check it before.
Also, with Hi input when I turn master volume up , I see big oscillation after half way.
Lo input behaves different, when master volume is half way open there is periodic squeal coming from somewhere propably from choke or some components on the board.
I suspect a faulty capacitor, I will try to find it.