2008 f150 misses or hiccups every 35 sec. regardless of RPM

The boat sat outside in a tropical storm, up to 50 mph winds. When the weather cleared I ran the boat and the engine hiccups, not sure if it is a miss. Tried to dry every thing out and found no water under the hood, though I think there must have been some. Ran it again today and the same 35 second hiccup no mater the rpm. Anyone ever heard of a problem like this?
thanks

You are in luck. Your CDI unit is bad. If you check the voltage to the TPS with the key turn to ON there is no 5V going to the TPS. This is per the service manual. I have this same issue on my F90TLRB that I just bought from a stupid azz marina. They said it ran fine at their marina so they will not do anything for me. The new CDI costs $400. I am waiting for mine to arrive any day now.

Vinh, Thanks for the CDI info. Have you received and installed your new unit. How she run? My boat is down in Baja and I will not be able to replace my CDI unit until October , when it cools down , down there. Just got back to San Diego an hour ago. Thanks again for your reply'

Vinh, a couple of questions. I have been looking for CDI units and I am not sure but it looks like Yamaha calls it " engine control unit assembly", and besides that , where did you order yours? This one is 1033.00 msrp. Thanks for your help.

SnorkleBob,
I received my CDI unit and install it and it still the same. I have another of the same motor and good running and it hick_ups on start up until it gets warm up then it stops. I removed my temperature sensor and it looks a little dry after I run the motor. I swap the water temp sensor from the bad motor to the good motor and the good motor runs fine. So it's not the water temp sensor. I then check the thermostat and it's bad. I cooked it in a pot of boiling water and it stays shut. A new one is on order. There aren't many sensors on this motor. I am waiting after I replace the thermostat then I will take the next step if it continues to hick up. The issue is not the CDI unit. I don't want to go thru and swap out every sensor on this motor from my good motor but it looks like I might to go that route to find out what's wrong with it. The compression are good and I cleaned the carbs. I think this is a temperature related issue. So check your thermostat first. If the thermostat is bad the motor won't warm up and it will cause the engine to to run lean and therefore caused the back fire thru the intake (hick up). The guy I bought the motor from said he replaced the water pump. I will check it tomorrow to see if that is bad also.

Today I want to rule out the carbs as the problem so I put the carbs from the bad motor into the good motor and it runs fine. Next I am going to check the fuel pump. If the fuel pump checks out OK then I think it's a mechanical issue and it's sticky intake valve. I am going to put it in the water and run the crap out of it to see it loosen up the valves. I've been doing a lot of reading online and surprisingly no one solved this problem on their motor. I am determine to get to the bottom of this. I let you know what I find.

Thanks for the info, it sure sounded like an electrical issue, with the 35 sec. hiccup at any RPM. This is really a tough nut to crack. My motor is fuel injected. I am thinking it may be a sensor that is on the "fritz". Eager to hear what you find. Good luck

I just removed the camshaft and check for the intake valves. They are all moving freely. My motor is a 2003 with carbs. I think it's a bad sensor. The manual shows an electrothermal valve for my motor that I could not find it. This electrothermal valve feeds to the CDI. I might have to cut up the shield for the harness to find out where it goes. I took the oil pressure sensor from my bad motor and put in my good motor and it runs fine. however I took a resistant measurements and they both have different measurements. I installed the oil pressure sensor from my running motor into the bad motor but I have not start the bad motor up yet. I am waiting for the thermostat to come back and check it again to see if that's the problem.

I removed all my carbs and clean them up. In the process I found out that one of the back end of one of the Jet was broken. I talked to a yamaha tech and he said that will definitely cause this hick up. That broken jet will caused too much fuel spool up at the base of that Jet and the carb can't suck up all that fuel. Therefore that one cylinder is running lean and it will hick up. For your motor since it is an EFI and I've seen a lot of people had problems with clogged injectors. I suggest you to first clean your injectors first and see how it runs. After I replace the broken jet I will have the dealer resynch my carbs too and see how it runs. I will let you know the result.

Thanks for the update, nice detective work. I was at Costco today and bought a bunch of injector cleaner. First thing I will do is dump several bottles into the gas and run it. Hope this cures your problem .

I replaced the broken Jet in Carb #4 and it ran perfect now. I didn't even need the resynch the carbs either. Good luck.

Congrats! A long hunt but I'll bet you learned a ton. I am waiting for my diagnostic software to arrive in a couple of weeks, than down to Baja in October to find and fix the hiccup. Wish me luck. I'll report than.

Yup. Expensive lesson $400 for the CDI unit. Now I have a spare CDI unit lol. Majority of the running issues are related to fuel problem. So install as many fuel filter as you can before it gets to the motor. I have a clear filter after the fuel/water separator. Any foreign particle gets thru the separator I can see right the way, including water. Good luck.