Right now I have a 1987 Yamaha 9.9 on the back of my jon boat. It really runs good, but it could use a couple of things. The mid section housing has seen better days, and the tilt mechanisms don't work very well. The handle is broke off which makes it more difficult to carry around if I have to. I found a used mid section for it which looks to be in really good shape. I would also buy the 15hp carb for it, I already have all the other parts needed to convert it. However, I'm not sure if it's worth sinking another $500-600 into a 29 year old motor. If I were to buy a new one, I would upgrade to a 20hp, but that would cost around $2500. So I guess my question is, which way should I go? I wouldn't buy the new motor until next season if that's the way I go.

Buy the new motor & be done with it. No more problems & double the horsepower. 

Sell the 9.9 for a few hundred to help fund the new 20hp!

I now see why you asked how my 15 HP does on the 1542. The 25 HP is about $600 more than the 20 HP I believe. The 25 isn't carburated and is the max power for the 1542. Personally, if I wanted to repower, I would go with a 25 HP. I don't think the 20 would perform much better than the 15 I have and I've heard of getting around 32-33 mph with the 25. Maybe you could find a used motor with some warranty left if you're waiting until next season. 

I had a late 80's 7.5 hp 2 stroke on my aluminum my grandfather gave me. I had it full tuned up when I got it as it had been sitting for a number of years. It worked without issue for 7 or so years. Then, it simply wore out. Needed a carb re-build every year and was temperamental. I was always working on it or bringing it into the shop. It was unreliable. I have a ranger and use that for majority of my fishing, but still like to go out in my aluminum boat for sentimental/quick trips. I was spending more time on some quick night trips working on the motor then fishing. I was able to get a few year old used mercury for a great price on craigslist and haven't had any problems since. Summers up here are too fast to be messing around with a motor. Get a new one and never look back. 

1 hour ago, zachb34 said:

I now see why you asked how my 15 HP does on the 1542. The 25 HP is about $600 more than the 20 HP I believe. The 25 isn't carburated and is the max power for the 1542. Personally, if I wanted to repower, I would go with a 25 HP. I don't think the 20 would perform much better than the 15 I have and I've heard of getting around 32-33 mph with the 25. Maybe you could find a used motor with some warranty left if you're waiting until next season. 

Yeah I was curious about what yours does with the 15, right now with the 9.9, 2 guys and gear plus battery and decks im getting 16 on the gps. I was also looking at the 20 to save weight over the 25. A new Suzuki 20hp weighs 97lbs, my 9.9 now weighs 87.

It might be worth looking into a newer used motor. You'll save over new and still have a good working motor with more power. 

I have decided to just buy a new motor, not sure if I'm in going to go with the 20hp or the 9.9 high thrust. With the Suzuki they are the same block, seems like the mapping gives the 9.9 less power though since its EFI. The other motor I was considering is the 20hp Tohatsu.

Don't get too wrapped up in the hp.  The CC size is more important.  A lot of companies use the same power head for different hp motors. If the 20 and 30 hp motors of the same make have the same CC, by the time you get the loaded to it's fishing weight, you will probably see very little increase in speed with the 30 over the 20 and both will get up on plane about the same, so it boils down to, most of the time you a paying several hundred dollars more for a couple mph.

You will see them down rate motors like Suzuki did so you get power and performance of a 20, but be legal where 9.9 is the max hp allowed. Both motors are probably closed to being an honest 15hp, but they get happy with the 20 numbers and cheat the system with the 9.9 numbers if they both have the same CC rating.  OMC/BRP did and still does that with their HO motors.  They take a 250hp motor, down rate it to a 225 so it will be legal on a 20' bass boat and call it a 225HO.

Tohatsu is a good motor.  They built the some of the smaller mercs for a long time and may still do.  The biggest complaint about them is the tend to get a little proud of their parts.

As for what size motor, If it does not stay on the boat all the time, get the one with the most CC want to carry.  If it stays on the boat, get the biggest one you can legally put on the boat and fish the waters you fish.  It's hard to go wrong with the max size, but it can totally suck dealing with one too small.