I have a 2000 dakar and I too dropped from 16 to 13 on the front. It did make the bike much better off road but caused the bike to stutter a little between 5 and 6'5 thousand revs (cruising speed). I don't know why, but I'm sure it was the sproket because it runs perfectly with the 16 back on.
I know surging/stuttering is a known problem on these bikes - I got mine reprogrammed when I bought it (it was 2 years old and did surge badly- but perfect after the reprog'),or whether it's because mine is one of the first of the 'injection' motors and not as refined as the later bikes I really don't know.