The breather for your transmission is at the very top of it - its the same 90 degree plastic fitting toyota use on every other automatic transmssion. It just sits there by friction fit only with a small O ring in it.. It has a rubber pipe which ends up at the filler tube itself (just like every other toyota automatic both front and rear drive) - You can buy that little breather from a toyota parts shop. its quite cheap.
I think your breather is dislodged from the top of the transmission and that is allowing dirt into the transmission.
When you were filling the transmission with oil, did the oil try to bubble/burp as you were filling or was it just pouring fast? - It should burp/bubble if you pour too quick, as that proves that the air is trying to come out from the filler tube (dipstick tube), if oil was quickly pouring in the dipstick tube, then the air in the transmission has another exit (usually the breather is popped off)
