Ticking/clunking Possibly From Brakes.... Help Please

Hi i have a mk6 pre facelift 1.25 fiesta, I recently experienced the following: on applying brakes, a fairly loud clunking noise coming from the front end. Checked calilpers and replaced pads and put on new discs. Still happening. CV joints appear good and when turning full circles at slow speed no noise coming from the joints. When on motorway, after about 5 miles driving, a low "ticking type noise which increases in volume occurring and this will clear if I depress brake pedal. It then reappears after a short period of time. The "clunking" noise is quite pronounced when applying brakes but the "thudding" noise clears when I depress pedal/apply the brakes. The replacement discs are not OEM and I have noticed that the stud holes on the discs are larger in diameter permitting a degree of movement of the disk. I am wondering if there is "movement" of the discs but having tightened (torque spanner) to the recommended amount, it seems unlikely ? I would have thought unlikely but when the car was jacked up and I moved the discs, was getting a similar noise when moving the assembly by hand. The discs are retained in place purely by the four wheel stud screw caps as you may know but wonder if one/both of the discs is/are already warped causing this thudding noise ? The CV joints have slight movement when car was jacked up and moved by hand ? Could it be the CV joints or is there something more sinister ? Calipers appear good and were well cleanedup at the time I replaced the discs. Any thoughts or considerations ? Cheers