If you just had it open, it's possible to have installed a bearing improperly. Hearing it in certain gears rules out the converter and pump by my thinking, however I have been wrong before, curious to see what you find, keep us updated.
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Well me and two of my buddies that build Allison's all the time went through it because I was scared of putting a bearing in wrong. Lol. And we had another trans right next to mine as we took them apart so That I knew how to put everything back together right. That's why I don't think it's a bearing. I think it might be the something with the pump being it was whining before this.