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I have had 2 yamies, very well designed and reliable engines. One of them was also a 25 HP... and yes there would be a very noticeable difference between a 25 and a 40... If you plan on any water sports like tubing, the 25 will really struggle if it will pull at all..:| Mine was on a modified V heavy duty Jon boat, still much lighter than a Whaler.

I would be looking at the weight difference of the 4 stroke vs 2... Could be huge depending on the engine..:o

The yamies of this size are not too bad, 115Lbs (version I had) for a 2 stoke 25 vs 183 Lbs for a 4 stroke 40... But still nearly 70 lbs difference hanging off the transom. On a 13 that may be significant.

An Etec weighs in at a whopping 240 lbs for a 40 Hp (same block up to 60 hp)

Few things to think about...:p