sorry guys ,a little new at this ,have a 1987 lowes commander,alluminum,been looking for motor,question is ,what is the difference in long shaft and short,will i be able to put a long shaft on my boat and still get into shalow water,im confused on which one to get,thank you ,,bassman

Shaft length is determined by the depth of the transome.  A 15" transome uses a short shaft motor, a 20" transome uses a long shaft motor and a 25" uses and Xlong shaft.  

If you try to mix them they don't work, a long shaft on a 15" transome has the anticav plate down below the bottom of the boat and a short shaft on a 20" transome won't have the water inlets in the water plus the motor will not get one plane

If looking for a used motor, stick to finding a Mercury, Evinrude or Johnson.  Start getting into other brands and you're gonna run into same major parts problems when you have to work on it.

I would probably add Yamaha to Ben's list