Since you are unfamiliar with cleaning these carbs, I recommend the Honda Carb Manual....Especially for this motor. The manual has a lot of pictures and shows you, step by step, how to clear the idle passages as well as the intermediate passages (which most people miss).
It also covers vacuum balancing, which is the last thing you do, once you put all the carbs back on the motor. Balancing makes a ton of difference at idle.
I think I saw someone say that the carb manual is out of stock right now, but I would still try...
http://www.helminc.com/helm/product...=&from=result&Style=helm&Sku=TM044&itemtype=N
JimmyD also found they are sold on ebay. One left
http://www.ebay.com/itm/Honda-Marin...anuals_Literature&hash=item3a7e14a296&vxp=mtr
The manual is well worth the $39. A carb job, done right, with final test in water is generally around $800 - $900, depending on parts needed. I always change the jet set (skinny tubes)...they are impossible to be sure that they are clean.
You mentioned changing jets and mods.....the only reason to change jets on a Honda is when you operate the boat several thousand feet above sea level. There are normally three different jets to use. The one thing I have found with outboards, is if you try to change from the factory standards, the motor will not last as long as it should.
Once you get the motor to idle, etc properly, then you need to see what your full throttle, trimmed out, rpm is. Then you can determine if the prop is correct or not. Once you get the overall performance zeroed in, then you should consider a small pitch prop for when you are pull the net or a load. It will essentially give the outboard a little lower gear (so to speak) for the pulling. It will overrev at top end if you try to go full throttle.
In general, 3 blade props are best at top end. 4 blade props are good for heavy loads and take off...getting the back end up quickly. Changing from a 3 blade to a 4 blade with the same pitch, generally will lower top rpm by about a 50 - 100 rpm. Changing the pitch but keeping the same number of blades changes the top rpm by 150 - 200 rpm.
Before spending a lot of time on the carbs....be sure that the compression is good on all cylinders and there is spark on all cylinders. Also check the timing marks to be sure they are in alignment. You are probably right on, thinking it is the carbs, but you will kick yourself, if, after you go through the work to clean the carbs, you find that you have a bad cylinder.
Mike