So how do I pull the transmission codes? I have an OBDII scanner but I don't think it will help with the codes.
You can give it a try, some transmission codes can be read with a cheap scanner, if nothing comes up then you'll need to have it diagnosed with the proper scanner. I've seen that kind of behavior on transmissions when the Transmission Range Sensor aka Neutral Safety Switch or Manual Lever Position Sensor goes bad; a bad VSS can cause that too.
Mine does this also I got some codes from it about a month ago then everything cleeared up and worked great now it is back. The codes I got were P1783 trans temp, P1705 tran rng out of test rng, P1502 vss inter apcm functioning, P1501 vss out of self test rn, and P0500 veh spd vss er. These seem kind of random or are they related through one sensor? It is totally fine when driving very easy. Fluid is like new still cause it keeps leaking a little so I just keep adding it as it goes to keep it fresh!
It looks like your fluid leak has caused intermittent contact with the sensors. I would inspect the connectors and sensors and give them a good clean with electric contact cleaner.