Well to save myself a full re-read here, I'll just say, if you put back in what you got out AND your car was running well before hand, I think there should be no strangeness post surgery. I only brought up the 4 quarts because it sounded as if you were unsure whether your car had someone futzing with your transmission prior to your working on it. It was in that case, that I wondered if someone didn't get enough fluid back in and was causing a noise you had a hard time putting your finger on.
To be frank, I don't know how much really should go in the damn thing or not, only that as it worked out for me, I had a car that was warm, not hot, got five quarts out and five quarts in and everything seems hunky dory. This is far from scientific, and the science-side of my brain is not being too nice to me for not have definitive answers, but the car several days later seems quite happy.