If the Tone controls are actively affecting your h/p jack (as the only
line-level output) as well as your monitor l/ss, the hi-fi should be deemed
to give a "flat" response at their *mid* or 0 position, so park them there -
then employ your Audacity digital eq and filters if you feel you have to.
The vinyl records should be cleaned of dust and free of static for this
archiving work.