Do you ever get a check engine light coming on and/or flashing when the problem occurs? Because it's ok in direct drive and not in OD, it's possible it's more a transmission problem than an engine concern....thinking something along the lines of a torque converter lock-up solenoid problem. Even if you haven't noticed a light coming on, I would plug in a cheap scanner if you know someone who has one and see if there are any logged fault codes. That would at least give you a starting point if there's something there.
Dentoman is right as that was a known issue as well, but again you should have a cel coming on and it should log a cylinder misfire code if a plug and/or coil are causing the issue. I also can't explain why that particular concern would go away when taken out of OD.
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