It just so happens I do have one of those basses, though I've never tried to go directly for his tone before. I put flats (Chromes) on my Ibanez so I don't think I'll be able to help emulate the tone, and I've got a Rumble 500 so it'd probably be slightly off anyway.
If you're looking for the Stingray tone this bass won't do it. The pickup just isn't far enough from the bridge to get a comparable tone. So I'd put it into the boosted jazz bass mode, so coil switch all the way down. No reason why you couldn't put it in non-boosted jazz mode though, I just preffer to get the volume boost.
Try it with the treble notched but cut it if things are too bright. Bass should be around 6, enough to thicken the sound without getting it muddy. Mids I'm actually unsure about for the bass. I remember them being pretty agressive with rounds so notched or a slight cut is probably going to be best. I'd probably pluck the strings just past the bridge pickup on the neck side.
Set the amp gain 12/3 o'clock (boosted/non-boosted), bass 12-1 o'clock (might need more on the little 40), start with both mids around 2 o'clock, add more high mids if you need more clank, low mids if you want more punch, treble at 12.
When using the OD I'd go for maxing out the drive and cutting back the level.
The key will be making the Ibanez sound like a jazz bass, and it will happily do that with a bit of bass and some attention to the mids. Picking closer to the bridge pickup should give you the attack you need. The higher gain should give you a bit of compression. And the OD set like that should match up nicely to his blended OD. The amp probably just needs some boosted mids.
It might not be a perfect match but that's where I'd start from if I was trying to emulate his jazz tone. Good luck!
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