Ok i was wondering why there is differant shaft length on surface drives going to MB site they list 3 different length's . In the process of building one know have housing machined both end's prop end still not welded onto shaft tube all dry fitted and my shaft is currently 38.5 inches long from end to end. My intent is to mount this to a 16 foot jon boat would it have anything to do with the turbalance ( for a better term) coming from under the boat just trying to get educated thanks

The longer shaft lengths are to help you reach down an get a better bite in deep mud

It also helps to get the prop in cleaner water for better performance.

ok thanks i assume that clean water means less wake or turbalance from the bottom of the boat

Exactly.