The best or accepted way was to run the manifold face on emery cloth which was on a flat plate or surface plate.
This would gradually reduce the high points.
If the amount needed was significant then a machine shop could machine it.
WD40 contains a mineral (petroleum) spirit as a carrier solvent. The mineral spirit WILL soften and swell natural rubber. It is ok to use on fuel and oil hoses but NOT coolant hoses and definitely not on door and window rubbers!
One way to get it (them out easily is to use a shop vac with really strong suction. First try without removing the vent. If they doesn’t work try a house vacuum with a long attachment. I have a 2001 Camry and my husband shoved a bunch of butts in there. Most likely to start a fire. Anyone know how to get rid of a jerk like that? He’s like a piece of gum ...