All of the power cables you mention are worth upgrading. The best bang for the buck is at the conditioner cable, because that feeds several pieces of the system at once.
As for the relative merits of A) spending a big whack on the power conditioner cable and using the stock cords on the audio gear, or B) putting upgraded AC cords on the gear and using stock on the conditioner, the answer is easy: none of the above. You have created an artificial dilemma. Just get rid of all the stock cords.
If, after that, you want to try a super duper cord on the conditioner, do it (and please make a note of what happens). Next, swap that cord with the digital source's cord and see which way you prefer things. Then please share your impressions!
As for the relative merits of A) spending a big whack on the power conditioner cable and using the stock cords on the audio gear, or B) putting upgraded AC cords on the gear and using stock on the conditioner, the answer is easy: none of the above. You have created an artificial dilemma. Just get rid of all the stock cords.
If, after that, you want to try a super duper cord on the conditioner, do it (and please make a note of what happens). Next, swap that cord with the digital source's cord and see which way you prefer things. Then please share your impressions!