I am in now way a transmission expert, but here is my input on it as I had a similar issue in the past and why I do not touch transmissions unless I absolutely know the history of them.
First question: Before you did it, do you know when the fluid was last changed and was it done regularly? By regularly, I mean every 50k miles or so..
Here is why. I had a GMC truck that had this exact issue. I know not a Toyota, but the 4L60E Gm Automatic is an incredibly reliable and stout transmission. It had 90k miles on it, so I thought I would drop the pan and do a fluid change. 500 trouble free and better shifting miles later I thought I did the truck a favor. Shortly after, I lost second gear. Shortly after, no forward go at all. The trans shop told me the fluid was never changed and I changed the environment in the transmission and it would have been better to just leave it at that point. The trans is used to the old fluid. A $2500 mistake to rebuild the trans. Ouch
There is always debate to do a flush/exchange/etc. and I always err on the side of no unless I know it's been done consistently.
This is my thought as to what happened, but obviously you won't know unless it's pulled apart.