Yamaha problem after hitting stump

Engine is a 2004 yamaha 50hp, 62y 1006609 f50tlrc.
I hit a stump, engine ran rough for about 5 minutes, then cleared up. Ran fine the rest of the day. Was out the other day, ran fine at first, then started running rough again. Sounds like a two stroke again.
I didn't hit anything this time!
Runs rough at idle, when you give it gas, it spits and sputters. It might go, it might die. If it does keep running, I'm not getting to wot. I do not know what that is, have no tach.
I took the fuel bowl off, there was sediment in it. Cleaned it out, put back on. Same thing.
is this a carb or efi engine?
If carb, one or more carbs?
How do I remove, & clean?
is their a main jet clogged?
i had a two stroke that I removed the carb, and rebuilt lower unit. I even put it back together, and didn't have any left over parts! LOl
any help or comments appreciated

First I'd check all the plug wires and make sure one didn't jar loose when you hit the stump. Check all wiring connections especially if it kicked up real high. Could have pulled something loose. My 04 iscarburated and has 4 carbs. Wouldn't think that would be your problem at first glance.

Everything I am reading shows that your motor is an EFI.
It is listed by yamaha as 2006 and later fuel injection type 1 system.

That said, here is my two cents. Check your prop (ensure it is not bent). You say running rough, just covering all bases (cavitation). Would also consider pulling the prop and checking the hub and spline. You did NOT say if you were in gear or not.

I assume that hitting of said stump jarred something loose within your fuel system (like you are already alluding to). I would check/change the inline fuel filter. The stump might be coincidence and you could have a plug or coil that is bad or going bad. Short of guessing or throwing a bunch of parts at it, might be worth finding someone with a computer to plug it in and quickly get the error code. Might save you a tone of time, headache, and money.

Thank you for the responses. I will check what was mentioned.

Runs rough in and out of gear. Really notice it in gear, under load.

since its a 2006 you may want to call around to a few repair shops to see who has the computer hookup & ask how much they charge and ask if they will deduct the computer read out& of course how much cost if they do the work. Could be a time & money saver in stead of guesses. Just my one cent............

I looked on yamaha s site. It looks like an 04 model. Also, they quit doing model year designations in 06. If I read it right, model year (after 06) is not significant to them. Model # is. Learn something new every day!

According to Yamaha a F50TLRC is:
F=Four Stroke
50= HP
T= Power tilt, trim, and start
L= 20 inch shaft
R= Remote control (console not tiller)
C= Model year 2004

A "D" at the end would be a 2005. They quit after that time.

You said it runs rough during idle and rougher in gear? still might be a fuel issue but... it could also be a bent shaft. I still think the best course of action is put it on a computer and let the diagnostics tell you what is right or wrong with the motor.

Had an 03 115hp four stroke Suzuki. Put it in reverse and with a lite throttle startered backing. Hit a log hard enough that it killed the engine. Restarted and when I put it in reverse it sounded like the reverse gear was stripped. Turned out that when it hit a caused such a jar that is moved the shift cable. Once the shop readjusted everything all was well. I wouldn't count it out until after you have a good shop look at it.

You didn't say if the motor stopped running when you hit the stump and how fast you were moving.
If your motor came to a sudden stop it is possible that the flywheel key may have started to shear off. That will throw the timing off enough to make it run rough. If you check the timing and it is off a few degrees you might want to check that key. :twocents

The previous comments are all good possibilities. Start with the simple ones first.
I would also recommend taking it to a good shop if you are not sure what it is.

Good Luck

Good one dfar.. I forgot about the woodruf key!

I hope that is all it is. Good luck