OK Burdie, best of luck and let us know how it settles out.
Just some updates on some diagnostic actions taken so far
1. Tube rolled back to stock one, with stocks opamps, still having noisy sound and weak bass on CD-in but fine on other inputs, so not the problem with tube and opamps. This was done with CDP coaxial out and notebook foobar2k over usb to matrix then line out to D1's both line in and analog in, then both SS and tube out to the amp
2. CDP to D1 (no matrix dac) via analog/line in, no luck still have that noise in CD-in input but lesser than having matrix dac in between. However, using coaxial or usb to get digital signal from sources CD-in has NO noise at all.
So i suspect is the line and analog in of D1 causing the noise, but why it only happened on CD-in but not on other inputs? I then try to look for any ratings differences on the inputs from my yamaha amp service manual, i think i found the reason why CD-in produce noise, this is mainly due to the design of yamaha amp (correct me if i am wrong), the CD-in do not share the same circuit board with other inputs, it has dedicated board with some opamps soldered there at which yamaha claims to reproduce or amplified more details from the source signal (if i read it correctly) and hence it amplified the noise from D1 which might be from the analog in, this might explain why other inputs have so such noise.
Now, back to the analog in, how do i ascertain that it is truely having noise which only an input of any amp having the so called better sounding can detect it. (ps i am not saying my yamaha amp is superior but in fact it capture the noise)