The transmission fluid is completely clean and fresh, no water in it thankfully. I suspect I still had about a quart or so of transmission fluid still left in the system before I refilled it, as I did not suck the fluid out of the cooler itself, only the transmission which I had already completely disconnected.
I did find that the front mounts had settled pretty significantly, which had altered the alignment of the engine. Thankfully I discovered this from removing and reinstalling the transmission. Just made the necessary adjustments and now the alignment is pretty good. My mounts are still serviceable, luckily, although not pretty.
