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Is the water coming from inside the cover or being spashed up by the mid-section? If from inside, check the cooling hoses.

When you say short shaft, are you saying it is a 15" or 20"? The older 13's take a 15" shaft.

If you can't find a 15" shaft, you can get a just the jackplate (no setback) for the 5" you need.
https://www.amazon.com/Cook-Mfg-50012...=CMC-50012

Photo installed on a whaler: http://thmarine.com/cmc-static-jack-p...allery]/2/