on my FT-1000D, the green LED "CW TUNE" on the display, flash also with normal noise, and in the earphone you can hear unwanted QRM caused by this ( when you turn the volume knob to minimum, this QRM still remain and you can listen him).
Unfortunately, there is no trimmer, no regulations of the level of the circuit Q3044-Q3045 led driver. Very fast solution is to disable this circuit, simply turning to the OFF position all the first 4 dip-switches in the top of the radio, named "CW-PITCH". Effectively, only the last two work on the BFO, the first 4 only serves to determine the frequency at which the led flashes.
For example, to pitch at 600Hz without QRM of the CW-TUNE led, only the dip n. 6 go to the ON position.
Obviously, the led CW-TUNE circuit lose his functionality, the led never goes ON, but the QRM disappear.