Wait.
Scott, did you say a misbehaving CDV? Did you NOT delete the CDV upon purchase? Because that would make the shifting hangups right then and there.
There is no filter to replace in the 6MT, but I'd look under the trans and see if perhaps you are leaking fluid slowly from the drain plug? It happens sometimes if the seal fails on the plug.
If you were in Jersey I could hook you up with a shop that would actually troubleshoot properly, and wouldn't just throw parts at the problem. They are the premier tri-state European repair facility, and do things right the first time. Its prob a 2.5 to 3 hr drive for you but might be worth it for Rolf.
www.redlinespeedworx.com - Ask for JR - He's one of the owners and a ridiculously certified tech.
But if you have the stock CDV installed and had the stealer replace the clutch because of the way the stock clutch system operates I feel bad lol