There's a thread running on the SD1 forum (I've got one of those too) re brakes, and in every one elses experience the SD1 brakes are awful, however mine seem excellent but I put that down to a fastidious previous owner rather than the inherent abilities of the system on the SD1 EFi.
I've found the brakes on my 2000 to be more than adequate and definitely haul you up nice and quick, that said they could be improved, it's a matter of personal taste where you go with any mods but I would maybe go for some braided lines all round, decent pads, and if they were available some uprated discs made from good material (slotted would be nice but not necessary) and not forgetting some good quality fluid, none of that new synthetic type rubbish "that doesn't take on moisture", believe me it is crap, fair enough it doesn't take on moisture........it boils away under braking long before that could even attempt to happen.
But remember, there are reasons the car was designed with what it already has on it. Proceed with care and common sense, you generally only get brakes wrong once. Sorry for the downer there.
I wish you luck getting to the bottom of your problem.