Apparently putting switch 6 up adds 100 pf to whatever the input capacitance of the phono stage is when switch 6 is down (which will be greater than zero, and perhaps a few tens of pf’s). As you indicated a load capacitance of 100 pf is recommended for your cartridge. Unless your phono cable is exceptionally short its capacitance together with the capacitance of the tonearm wiring and the input capacitance of the phono stage with switch 6 down will almost certainly total around 100 pf, and very possibly more. Therefore the most accurate performance of your cartridge will most likely occur with switch 6 down, although it is possible that having switch 6 up may be subjectively preferable, or as Halcro said it may not make much difference either way.
Whatever difference load capacitance may make will occur mainly in the treble region.
Switch 5 should be up and 1-4 down, of course.
None of this will affect the hum or fluttering woofer issues you mentioned. Is there a ground wire connected between the turntable and the phono stage?