The best advice I ever got on this topic was from Splatt on TGP but, I'm sorry, I'm no David Torn (not even 1%!):
ebow NOT placed directly over the chosen-pickup-in-use.
volume pedal, bridge pickup, tone ctrl rolled-down to some degree.
a clean, open amp-tone --- something that simulates hollowness, air.
i never use a pick for these kindsa sounds; i use the flesh of my RH fingers, in conjunction w/the volume pedal.
focus on the idiosyncrasies of flautistic phrasing, phrasing w/breath.
dt / spltrcl
So I'm looking more to some effect I can just dial in. (I use a Line 6 M13 but stand alone effects are cool, too, once I know what I'm looking for in that regard, I'm sure I can find something ballpark on my M13).
The tone I'm shooting for is the flute-like tone Jerry's getting on this video at say at 5:32 and (especially) 6:04 (at 6:04 it sounds like he might be using an octave-type effect + something else):