2002 90hp yamaha rough running

[uwantscuba]

Ok, here's the history first and soory for the long post, but I think it may be important. My 2002 Sea Pro 18' CC ran well thru 2007 and I always changed the impeller every 2 yrs and new plugs every year, but no other maintenance was done. I believe I fogged the engine each year and at the end of 2007. Never went out in 2008. I drained most of the gas in 2009 and added new fuel (87 octane) for the 2009 season. Boat fired right up and ran fine. Fuel sending unit went bad and I ran out of gas once in 2009. Fixed sending unit and only used a one more time in 2009 and had the same problem as in 2010 once, but ran fine for the rest of the trip. In 2010, boat fired up and ran fine, initially. On first outing in 2010 while at WOT for about 5-10 min (after running fine at idle and during trip out to the fishing grounds), engine suddenly bogged down and died. I thought I had some water in the gas because it took quite a bit of cranking to get it to start stumbling and sputtering and eventually start while manually feathering the throttle at the carbs. After a half hour of this, I got it to run enough to get into gear and could get it to pick up speed and stop sputtering by quickly moving throttle lever forward and back quickly. After finally picking up speed, it sounded fine for another 5-15 minutes of running WOT, then it bogged and shut off again. Cranked and Cranked while manually feathering the throttle linkage at the carbs to get it running again. Once started again, we made it to the dock without sputtering or stopping. Only used once in 2010. Now 2011, decided it was probably gunked up in the carbs. Bought rebuild kits for each carb and had my cousin (who is think is knowledgable about marine engines and only down my location for a day) help me clean, rebuild, and install the carbs. We found a lot of sand looking stuff in the bowls, which he said looked like corrosion. We made sure all passages and small ports were open by passing a small brass wire through them. I installed a yamaha fuel/water seperator and a clear fuel filter (pre-primer bulb) to see if anything is getting past the filter. Tried starting. No start until I used starting fluid. Got started, but spitted and sputtered. Would shut down if I didn't manually feather the throttle linkage at carbs. Sounds like it's missing, but no different than when I had those problems on the water. Except now, it doesn't start running fine after a bid of feathering the throttle. Pulled the carbs again and used thin brass wire to check all passages, all good and no more sand or gunk in bowls. I also cleaned the fuel enrichment device, which had some of the same sandy gunk stuck behind the plastic housing behind the diaphragm (not a complete closing at all, but it was there). I also replaced the diaphragm and gasket in the front of the fuel pump just for good measure, even though everything looked good. I pulled the inline fuel filter and had sandy gunk on the screen, so cleaned it too. All fuel lines look good. Put everything back together today. Engine started after a bit without the need for starting fluid, but still sounded like it was missing. I used a spray engine restorer, spraying into carbs until almost entire can was used (as directed on can and smoked up the joint). Can states it removes gunk from piston, valves, etc and restores engine power. Waited the directed 30 min and restarted to run it out. Engine ran and once major smoking stopped, it was still sounding like a miss. Fairly regular, but also had some sputters added in here and there. I'm stumped. It happens at idle and causes a stall, but it also happens when I add a little manual throttle (no more than 1500 rpm, since I'm only using muffs for water source. What do you think is wrong? electric (it has CDI with Micro computer control? I was told by another mechanic that this engine 2002 90 TLRA does not require timing and synch unless you mess with the linkage or screws, which I have not. HELP! My next thought is to send to a professional. I don't have a compression guage. Anything else I should try before spending the big bucks? Again, sorry for the long post.
Steve

[uwantscuba]

Also

Also, I bypassed the fuel tank with a new 6 gal. tank with fresh fuel (87 octane with Sea Foam added). New fuel line, bulb, and connector at engine, so entire boat fuel system bypassed.

[200090tlry]

Pretty obvious

Your going to need to clean out fuel system and clean out carbs. Also a good carb job includes new Fuel Pump $40 bucks. Also never spray carb starting fluid in outboards you should only use gas mixed with 2cyl oil. Washes off oil in cyl. You can use deep creep or any outboard cleaners like omc,yamaha,mercury without issues. Taking apart carbs is pretty easy with good flashlight and time/tools work bench. Do one at time only no mixing parts on carbs. Part that opens butterfly metal shaft pops off with screw driver. Oil rubber parts after cleaning carbs, I used CRC fuel injection cleaner or there electrical cleaner. Pure carb cleaner could be problem with removing laquers on metal. Also use scribe 1 2 3 on carbs to keep that straight, mine was done already. If your carbs are done now what setting are pilot screws 1 1/2 turns out that's 360 degree's plus 180. Some people think half turn is one full rotation so I go degree's. One you have 1 1/2 try turning in 1/4 turn then run so 1 1/4 now. Mine stalled at lake as well at 1 1/2 turns out after cleaning. Go to put in gear and stall. Once I leaned it 1/4 turn she ran like rapped goose. Doing a comp test is easy I pulled the landyard think that's all you need to do to kill power to cdi's. I hope this is ok or another option ground out each plug wire when doing it. I would check harbor freight and please post your numbers and if your stalling stops with my suggestions. Get new plugs if not already done

[99yam40]

best thing to do is get a Yamaha service manual for your motor and the proper test equipment. Start with the basics compression, spark,and timing. Then it is on to the fuel side if all else is good and in spec.
The inputs and outputs of the CDI can be tested and will show if there is a problem with the ignition system.

Fuel pressure and vacuum can be tested easily to make sure you do not have too much restriction in filters and lines and you have the proper pressure.
but when you clean the carbs all of the system needs to be cleaned at the the same time or junk just plugs up what you have already done. Switching to new tank and lines is great as long as you clean everything else once you do. This includes pump, lines, and carbs.

The sand looking stuff could be the lines coming apart from the ethanol or something in the tank itself. Ethanol acts as a sollvent and loosens everything from inside tank and lines, which ends up in the carbs,
Once the carbs are clean and reinstalled, the link and sync procedure needs to be done every time like the manual states, as the carbs do not end up exactly where the were.

As long as this thing has sat up, the carbs probably need to be cleaned professionally with an ultrasonic cleaner

[rodbolt17]

you have to do the fuel system not just the carbs.
any debris prior to the carbs will instantly refill your carbs with debris.
first check compression to see if you leaned it out and popped a piston.