Ya that's what I'm slowly figuring out - it's too slow 
Maybe the new Arduino Due would be able to do the trick if I can get a hold of it?
A logic analyzer would have been perfect, but yes, that's exactly what I have to do - sample over a long period of time and analyze afterwards (and the analyzers I have looked at can not hold nearly enough samples).
I do have access to both ends. My plan, though, was to generate a pseudo random sequence of bits and send them from my laptop. So I'll have that particular sequence stuffed with start and stop bits from my laptop's UART. Then, obviously I know what the sequence must be and thus can compare after receiving.
pylon, not such a bad idea but involves a lot of implementation work! If all else fails I'll look into it.