First, private citizens cannot indict or formally file charges under federal law. They can file reports or complaints with a U.S. attorneys office, but it is up to a prosecutor as to whether or not to actually bring federal charges. So to the extent they are trying to act as some kind of private criminal prosecutors, they lose right there at the outset.
As for your argument about the number of federal districts...this is why I hate debating with non-laeters because most of them have no idea what they're talking about when it comes to legal process, courts, etc..
There are 94 federal districts, but the vast majority of those have multiple judges and multiple courtrooms. In fact, maybe there is some weird district that has only one, but if so, I don't know where it is. So yes, there are over nearly 700 actual federal judges who preside over their own court, and you only need one to get a conviction and, under your theory, remove a President from office.
NOW, it's...700 actual federal judges...