Definitely a weird clacking noise, but doesn't sound like it is something serious to be concerned about... I hope
Not sure what it would be though, that's always hard to track down.
Your AEM fuel pump is supposed to be designed to withstand Ethanol no problem, but I have no experience with aftermarket pumps so I can't say much there. I just have a feeling it doesn't have so much to do with the fuel that sat in there (which you drained), but rather that something may be faulty.
I wonder if it would actually be helpful to just get a custom tune started right now to see if it solves your problems. Because with some of your aftermarket stuff in there, and a fresh rebuilt engine, something just doesn't seem to be quite right. But you had it running prior to the rebuild, so it doesn't make a lot of sense.