Update! Filter was sludged up, and had remnants of a speedo gear that was lunched. Drained, refilled, and threw a pan with a drain plug I had laying around on it, and it shifts great again. I drove it around for about 20 minutes and had no problems. I know I am not out of the woods yet, I will probably drain and refill again after I drive it around for a while. There wasn't any shavings in the pan or filter, but I am still scared of what may be helping to plug the filter. Thanks for the advice!