It felt like i hit a log

I have a 1996 Johnson 225 Ocean Runner. I just bought it a month ago with the assumption that it has between 1600 to 2000 hrs. with regular maintenance. It wasn't running and had sat up for about a year. I drained old gas, changed water separator and fuel filter,changed out spark plugs with NGK (which is what the previous owner used). Changed two of the plug wires, water impeller, and lower unit oil. Disconnected the VRO and mixed the gas. It was hard to get it started but got it running and used seafoam spray directly into the carbs. Smoked alot but finally cleaned up. It has ran fine the last few times I took it out. Still kind of a pain to get it started since the primer solenoid fires only when it wants to. I'm thinking its problems with the switch, and not the solenoid. The engine idles and shifts fine. It gets on plane great with no missing or sputtering. After running a few hundred yards down the bayou, it starts missing intermittently like it loses fire in more than one cylinder, maybe all 6 but then catches back up. The first time it happened, i thought i hit a small log or lily patch. Slowing down helps it but it will do it at any RPM if you give it enough time. I worried mostly about the transom since the boat is a 1993, and its pretty violent when it keeps jumping around. The previous owner told me that the kill switch doesn't work, so you don't need to put the plastic spacer under the key to start it. Wondering if its possible the kill switch is affecting this. The engine wont shut off until you turn the key off. Has anyone had this issue before?

Well-----I would be taking the gearcase off to check shift rod adjustment.-----Did you by any chance turn the shift rod when lower unit was off.-----Perhaps it is jumping out of gear.---Myself I would take gearcase apart for inspection.-----Easy for me to do and say that.

No i'm pretty sure the shift rod wasn't turned or moved. The boat has a 80 Gallon fuel tank and I have filled it up twice and ran the boat since I removed the foot. I haven't came across this issue until two days ago. I forgot to put in the post that I did drain the battery to almost dead trying to get it started so i bought a new battery the day this started happening.

The battery has very little to do with the ---" spark making system "-----Perhaps inspect the flywheel magnets.-----Perhaps test run with a timing light hooked up to cylinder #1 and observe the flashing light.----Repeat test with other 5 cylinders.----Test the primer solenoid ( very reliable item ) or perhaps use the primer in manual mode with the red lever.

My guess it's spark related. Have you done the gap jump test....need a strong 7/16" or more crackling ........in Joe's words: "lightning like spark". I personally doubt it's a lower unit issue....but you never know. Thoroughly drain gear oil and check for excessive amount of wear particles. Refill from the bottom until it leaks out the top opening/vent/level.

Cliff, first off let me say I have no experience on the motor in discussion. However, I have lots of experience on other motors where the customer says "it felt like I hit a log". That is a classic statement and the almost immediate thought we outboard mechanics get is it is jumping out of gear, turning half a revolution, and slamming back into gear with a mighty thud. I'm sure that is the reason for racerone's response in reply #2. Listen to him.

It's hard to "feel" what Cliff is describing, but for me its not gearcase. Here is a quote from his post:
"After running a few hundred yards down the bayou, it starts missing intermittently like it loses fire in more than one cylinder, maybe all 6 but then catches back up. The first time it happened, i thought i hit a small log or lily patch"......
Looses fire in cylinder???

I appreciate all the help. I pulled the key switch off to check connections since the kill switch doesn't need to be put in to run the engine. Just seemed fishy to me. One connection was barely holding on, and another was broke inside the connector where it is crimped. I will get these connections fixed and check to see if the primer solenoid works consistently. I will try to get it in the water and try it again. I was also thinking to rev the engine in neutral to a high rpm and see if it still does the same thing. If so, the lower unit shouldn't have anything to do with the problem. I will try to get a video of what is happening uploaded on here. It's not very long but it does show it jumping around and the sound of the engine. As far as the spark test goes timguy, No i haven't done that. I'm assuming you are talking about pulling all plugs and holding one plug at a time to the block with a pair of pliers? Racerone, i don't have a timing light. Is there a certain one i can rent from o'reilly that will work? It really sounds like more than one cylinder is dropping out, but runs fine at idle and lower RPM's.

Fact-----Just don't rev it up in neutral to see what happens.-----Unless you have a few baskets and boxes to gather up broken motor bits.----I think I will step aside here now.-----Other folks will help you I am sure.

Ok well i can't figure out how to get this video uploaded. I will get the wiring straightened out on the key switch since it is cheap and easy. Check the magnets under the flywheel, sparktest, and drain oil from the lower unit before running it again, then update with what is found.

For spark test you don't use plugs but make or buy a "spark gap tester". Mine is a couple finishing nails in a piece of wood. Gap is adjusted with a small alligator clip. Expect that crackling 7/16" minimum lightning like crackle.

Thanks timguy, I bought one but I found one of the coils on the stator was very loose and coming apart. I am waiting for the new stator to come in. At the time I didn't think it was related but I was having issues with my tachometer and fuel gauge going crazy. I read in a post that the charging coil in a bad stator could cause the tach. to give false readings. I'm hoping this new stator will fix more than one problem. I will definitely be checking the fire once I crank it back up though.

This may be your fix. Will wait for the report, thanks.

Well Timguy, the stator was definitely the problem. I also found that the voltage regulator was not putting out voltage so I have changed that also. The tachometer is now stable and the engine starts right up after holding the key in and priming for about 10 seconds. The only thing left to chase down is the "beep" when the key is turned to the on position. This was working and the check engine lights would light up, and then go out. Now the lights run through their sequence, but the initial "beep" is gone. I will have to research and see what wires are in that circuit. I may have pulled something loose while wiring up the voltage regulator, but I would think that wiring circuit would not be in the same area. Do you have any knowledge on this circuit?

Pushing the key in for 10 seconds is not needed.------The primer is a valve and NOT a pump.------Key is to be held in while cranking for near instant starting.

Thanks for that. I read somewhere that you needed to hold it for 10 seconds.