On outboards is a short shaft or long shaft better?

I have a 14ft row boat that had an older 9.9 on it and the top speed was 8 with two people, gear, two batteries and a front deck. The motor was a short shaft. When I went to my cottage we own a long shaft 9.9 merc which is significantly newer. With two people three batteries and 6 gallons of gas the same boat went 13.5 on gps. I was wondering if the increased speed is due to the newer motor or because it has a longer shaft?

Thanks

-Dylan

Could be a number of things...  load balance, new motor, weak older motor, transom height, fuel in the tanks old or bad, etc.  

Different shaft lengths are offered because some boats have to mount them differently and at different heights.  Sailboats come to mind as often needing long shafts, due to where and how they are mounted.  Most small aluminum & Jon boats would take a short shaft.

Well a few of those things can be eliminated. Load balance was the same because I just took the old motor off and put on the newer one. Transom height was the same cause it was the same boat. The fuel for both the engines was all purchased at the same time. So I am thinking it is most likely because the engine is much newer (a 2003 compared to a early 70's). I was just thinking shaft length might make a difference because the prop was deeper down.

Well a few of those things can be eliminated. Load balance was the same because I just took the old motor off and put on the newer one. Transom height was the same cause it was the same boat. The fuel for both the engines was all purchased at the same time. So I am thinking it is most likely because the engine is much newer (a 2003 compared to a early 70's). I was just thinking shaft length might make a difference because the prop was deeper down.

Engine horsepower ratings were measured differently in the 70's compared to now.  Before they were at the power head and now it's at the prop shaft.  The changeover occured somewhere around 1980.  There were a few boats that got their max HP rating lowered after that went into effect.  

Lets not forget prop dynamics (unless both motors also have identical props).  The new motor probably has a more efficient prop too that can account for some of the difference.

Generally the less of the lower unit you have in the water the faster it should be due to less resistance with everything else being equal.  Unless that longer shaft helps lift the boat up on pad higher so there's less drag on the boat when its "on plane".

The shaft length is detemined by the transome heigth.  A long shaft (20") motor would run way too deep in the water on a short transome (15") boat.  A short shaft motor would not work on a long transome because when it started getting up speed, it would have the lower unit mostly out of the water.     With the proper length motor on the boat, the anticavitation plate should be approx even with the bottom of the hull.

No way can you compare the power of a newer 9.9 to an old 60's 9.9.  Even if the older motor is in like new condition, the newer motor has approx 15% more hp because of the way they are rated.  Figure the age and wear, it may have 25% or more hp.  Add the advances in prop design and there is just no real comparison between the two motors.

Way2slow is correct. The older motors were powerhead rated and the newer motors are prop shaft rated for the HP. He is also correct in the shaft length determination.

By you installing a long shaft motor on a short transom boat, you are not going to get the best performance because of lower unit drag.

FYI,  A friend of mine was in the process of buying a 14' Grizzley jon boat and already had a short shaft 8HP motor for his present jon boat. I asked him which boat did he order and he said the 20" tansom model. I reminded him of the motor shaft length, so he changed his order to the 15" tansom model.