I'll look into this Salae LA, sounds particularly useful.
Unfortunately it is the bit error positions that are just as important as the error event itself because I need to make a statistical model of the channel (as part of my Master's Thesis). The errors would usually occur in bursts and thus the positions of the errors to observe these bursts are quite important. Maybe another way to do it is have a counter count the number of bits between errors and when there is an error, save the counter value then reset the counter.
I'll also see if I can get a hold of the Due as soon as possible.
Thanks for your help! I'll post again if I get it to work.
PS I hate assembler!