I know it will never be perfect but is there a standard method for aligning a print head so when I want to print with a border it's as squared up as possible? I use an Epson R2880. For example if I turn off expansion and add some margins I get a nice white border but its slightly uneven. I could do it by guessing and tweaking margins but I'm not sure it will translate to larger prints. Basically I want to know if there is an easier way than eyeballing it?
From what you've said, the margins are never consistent, which implies that the paper handling isn't working quite right -- whether that's due to a guide not being pushed flush against the paper, or a fault with the device is impossible to say with certainty without physical access to the printer.
Had it been a systematic error, then you can always measure (if it's always off by half a millimetre or so), and take this into account when setting the margins.