Well, you're experiencing the same thing that so many other AOD owners have before you.
I have the same problem in that, on occasion, when I shift from 1st to 2nd and don't pull the shifter back into 1, the tranny seems to pretty much skip 2nd alltogether and go straight to third. This can be avoided by doing as tireburner suggested; however, in my experience, if you wait any significant length of time, the tranny wants to shift into third early.
You're going to just have to play with the shuffle and figure out what works best for your tranny.
The best solution, of course, would be to buy a Lentech valve body. I'm getting one in April for my AOD. The Lentech unit allows instantaneous manual shifting for the AOD in 1st, 2nd, and 3rd. Overdrive is locked out electronically until you want to use it (cruising on the highway). At that time, you flip a switch, and whoala....overdrive.
--nathan
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'91 GT, Coast 347, 9.5:1 compression, full intake, Wolverine 1087 cam, exhaust, Keith Craft ported Windsor Jr. Irons (235 cfm intake, 195 cfm exhaust), AOD, PI 3500 converter, Lentech valve body, 3.73's (4.10's in the works), and Yokohama ES100's out back.
Daily Car: '04 Infiniti G35 Sedan 6MT
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