You can get bottom end bearings no problem, just source them outside of Ford. There is a healthy performance aftermarket for these engines, so rebuild parts shouldn't be an issue.
As for the oil filters, assuming a person uses the correct filter, there shouldn't be an issue. I know when these Duratec motors first came out some parts places were using the older focus filter off the Zetec, the FL-400s. These are longer then the correctly speced FL-910, and led to some curb strike issues. Once the word got out however, I don't know of any further issues. Like another poster said, you'd have to pretty much rip off the front bumper and radiator supports before you'd get to the filter. The filter actually sits higher then the subframe, so even if you got the car airborn (which I have

), it wouldn't come crashing down on the filter.
As for the noise, its hard to tell. The audio in that video is pretty distorted. It honestly sounds like bottom end noise to me, however it could also be the injectors. Its just too distorted IMO. I live with injector tick everyday on my focus, and it sounds nothing like that...but like I said, the audio is a bit distorted.