Sudden thunk coming from motor when getting on plane

Motor info: 2012 yamaha f150 with 337 hrs.
I just serviced the lower unit Saturday and ran it for the first time today, after about an hour on the water (some spent running to other spots with no issue) I went to an area with a lot of current and the wind kept pushing me toward a jetty so I was bumping the motor in reverse quite a bit to keep my distance. I did notice several times while putting it in reverse that sometimes it made a slightly harsher sound than normal.. Nothing severe but just enough of a difference for me to take notice, I attributed the cause to the current thinking maybe it was spinning the prop while in neutral. I left the spot and slowly pushed the throttle forward to get on plane and before it got on plane and while increasing the throttle slowly there was a noticeable “thunk” that could be heard and felt. Nothing violent or loud just noticeable.. I though I must’ve hit something like a small branch or some other debris in the inlet (which by the way is about the best way to describe exactly what is felt and heard.. a light strike to the lower unit by something in the water). So on to another spot again drifting and the wind required I put the boat in reverse several times… when I left same thing the thunk occurred in exactly the same manner as before. It seems to be the theme that whenever its been in and out of reverse and then then I go forward the thunk occurs. I tested this by coming off plane and putting it in forward and back on plane several times and it did not make the noise, then I would hit reverse several times then back on plane in forward and 2 outta 3 times I did this it made the noise. I have been racking my brain trying to figure out what is happening and why the sudden onset of it.. It would be different if I could come up with some reasonable cause like hitting bottom or some other out of the ordinary happening to explain the cause, but nothing has happened different than normal. The only change between a week ago when it didn’t do it to today is I serviced the lower unit (gear oil & water pump). I was talking with a friend and he was thinking something along the lines of the clutch dog not engaging quite all the way and was asking me if I had turned the shift shaft on the lower unit at all when I had it off changing the water pump.. I am pretty sure it didn’t get turned the only thing I did to that area was wipe off old grease and apply new with a small brush. That did jog my memory about something though… when I put the lower unit and prop back on I spun the prop and lower unit made a clicking sound. I found the shifter was not all the way in neutral… it was barely forward of neutral… I must have bumped it while in the boat earlier before I took it off. Is it possible the shift shaft on the lower unit moved back to the normal neutral position when I removed the lower unit, but because the shift shaft was slightly in forward when I put it back on that its maybe like one spline out of alignment and not getting complete travel sometimes in forward to ensure lock up of the clutch dog?
"FISHUNTR"- 2012 20' Pathfinder, Yamaha F150, HDS gen 3 9T


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