The LFO is disengaged when the switch is set to filter only so you should definitely not be hearing it then. And certainly not in bypass. Are you sure you soldered the 3pdt toggle in the right way?
Other things I would look at with noise in bypass - wiring and power supply. More details and a pic would help here.
Other things I would look at with noise in bypass - wiring and power supply. More details and a pic would help here.
Luckily I got that out of my system.