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

Yes, absolutely replace the manufacturers jumpers, especially if they are those uninsulated bars.

I can also recommend trying to connect the positive lead from your speaker cable to the positive lead on the tweeter terminal and the negative speaker lead to the negative woofer terminal. It may make an improvement and is free to try.

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. 

Of course! Even molecules soon can be upgraded ye kiddin' me?

The Vandersteen website has some great info under the faq portion regarding biwiring. So does Audioquest. I recommend biwiring your speakers if the manufacturer has gone to the detail to develope a high quality crossover.

As for manufacturers jumpers, I recommend replacement. Using the same cable manufacturer and exact cable construction as your speaker wire. Additionally, Nordost’s website has examples of different jumper configurations.
Google - nordost jumper cables pdf -To split or not to split -



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I agree with viridian.
Also, you can easily make your own jumpers out of the many bulk speaker cable or hook-up wires available.  Put a spade connector on one end and a banana on the other so you can attach them without interference from your speaker cables, regardless of whether your speaker cables use spades or bananas.
Finally, if you plan to keep the speakers for a long while, consider removing the binding post plate and soldering the cables to a single pair of binding posts for the best connection, then no jumpers are required.