Have been experimenting quite a bit with PT2399 based effects.
Have tried many of the existing methods, vactrol on pin6, voltage controlled current source on pin 6, modulating pin 2 ( little angel chorus ).
Something came to mind that Id used previously to modulate XR2206 function generator. Like the pt2399 the operating frequency is determined by a resistor sinking current to ground. By attaching a voltage to the other end of this resistor instead of returning it to ground, this permitted voltage control.
Anyway a picture tells 1000 words so here:
The 100K pot is a matter of taste, it permits very long and gnarly delays and with modulation sounds pretty insane. A more sensible choice would be 50K. Only a fairly small wiggle is needed at the bottom end of the pot and with the values shown a few volts of modulation will produce a sizeable change in the delay time.
The rest of the circuit ( not shown ) is just the basic echo circuit from the datasheet.