If your 100% sure the surging probelm is gone, then ignore this 1st paragraph... if not, like I mentioned earlier... get a portable, (6 gallon) gas tank and connect it after the boats main filter, (Racor?). This will eliminate the boats entire fuel tank/system. You might have a kinked/restricted line, restriction in the tank pick up, sediment/crap in the lines... a venting problem, etc, etc. A fuel line that's kinked, or has a build up on the inside wall, (this has happened in some cases due to ethonal) has the effect of a smaller diameter, (ID) fuel line, which can starve the motors vst tank and cause surging. In any event and again... only if it's surging, it's worth doing to prove wether it's the motor or your boats fuel supply.
With the surging problem out of the way, the first thing I'd look at is your throttle linkage at the motor. Make sure the cable adjustment nut hasn't come lose and moved, (see figure) -
http://www.boats.net/parts/search/Yamah ... parts.html
Disconnect the cable connection, (if you have to) to make sure the throttle cable is traveling far enough to match the throttle linkage travel. Have someone move the control lever while you check it out at the motor. I know it's a long shot, but maybe a piece of hardware/plastic/junk, who knows?... got lodged around the linkage area and is resticting it, or something just might be jammed. I think items 27, 34, and 37 control timing advance, so make sure they're not restricted. Lightly grease any/all linkage points.
Another item you can look at is the belt that drives the fuel pump. Just wondering if it were worn/stretched if it would cause your problem.
Item # 10 -
http://www.boats.net/parts/search/Yamah ... parts.html
You should see somewhere around 5300 to 5500 max rpm's, (depending on load). No tabs, trimmed up a bit.
After that, I'd do like BobP said... dealer time.
