shortscale guitars were originaly sent out of the factory with like 12's or something like that.(thats vintage, not the new stuff)
there are a few videos on youtube that show how to effentially setup a stock jaguar/ jazzy bridge.
also, fender sent out the jag with a factory shim in the neck pocket, this increases the break angle over the bridge as well as bridge height making more tension in the long run over the bridge.
in a nut shell, if its a jap, shim the neck with a playing card or peice of a pack of smokes.
watch a couple videos on youtube and fiddle with the bridge.
the best one i can think of is one done by a fellow named hurb from the shortscale crew, he has like 5-6 jags and jazzy's and the video shows him setting up a 69 jaguar.