I prefer 4 stroke for a couple of reasons, first they run cooler and last longer. But secondly they don't burn oil and put that exhause into the water that I want to eat fish out of.
I did, however put a new motor on a very old boat (1963), so I did have the option of being picky. You are looking at a used motor, so you don't have the flexabability that I had.
However, if you find the boat you are looking for that doesn't have a motor it will be VERY cheap and you might be able to get a new motor on it for a comparable price (boats.net has some bargains), while getting what you want; or close to it.
That said, if you find a deal that is too good to pass up don't pass it up! Prices will go way up in spring and you won't have time to modify it to your desires before ice out. The big thing is always of course the condition of the motor.
Oh, and I am a huge fan of Yamaha; I have had lots of problems a couple years ago - but EVERY one of them was north of the power head.