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

I sort of agree with czarivey. There is a lot of snake oil in the cabling business, in my opinion. 
Though you have a pair of Cardas, I wouldn't be slavish and get a matching pair, especially if the cost was not affordable.
There are many other cables out there that should do the job.
Of course, you are introducing variables, but why not enjoy the ride?
FWIW, a set of Zu's would not be a very costly way to go. Try them on the low frequency side and then reverse with your Cardas. You might be surprised.

Though I am not familiar with the Square 5s I am familiar with Wilson Benesch and they are a company that is all about the details. If they supplied jumpers then they must think that they are good enough to represent their name. I would not make this statement about most speaker manufacturers but WB is a particularly dedicated company. I would try putting the speaker cables on the high/mid posts and jumpers to the bass posts. However, we all love to experiment and different jumpers or bi-wiring may end up being your preference.

chrisr said....." is there a SINGLE speaker manufacturer advocating changing the provided jumpers?"

Well...yes... as a matter of fact,there is...Heres one. And there are probably many more...

From my Sonus faber speaker manual...

BI-WIRING
This type of connection improves the general reproduction quality, and in particular the bass frequencies. This requires two pairs of speaker cables used in the following manner: remove the connections between the terminals (bridges) ( g.11), connect each pair of terminals (high and low frequencies) independently to the amplifer as shown in g.12.

Actually, the question was not about the benefits of bi-wiring, it was about benefits of replacing the jumpers.

Yes upgrade them soon will improve your sound.