Jumper Cables - use the stock or should they be upgraded ?

I would never have believed it, but changing the jumpers may change the sound. When I had my Harbeth SHL5's, changing to Audience AU24 jumpers cleaned up the somewhat boomy bottom end I was experiencing and made the bass pitches much more defined.  But different isn't always better, so I would suggest trying some aftermarket jumpers and seeing if they improve the sound to your liking.  BTW, when I had my Opera Callas speakers, the aftermarket jumpers rendered no improvement whatsoever.  So that pretty much sums it up, IMO. 

Whilst we're on the subject, jumpers aside, different results may sometimes be obtained from connecting the single wires to the upper or lower set of binding posts.  Some do one upper and one lower.  It's worth a try.