I knew there was wood in there. As I said before, my friends boat was as pretty as yours. But that wood was rotted. I'd still make sure its OK. Its easy to pull a screw and check
While there is a possibility there is no wood there. I find it hard to belive. Never saw one without. The thickness of your transom exceeds that .100 spec they show. Take out one of them screws and poke in there.
A friend of mine had a similar issue. What you can do is loosen the top channel, just take the screws out without removing the motor. Take a very long screwdriver or stiff wire, push it down through the screw hole. If it keeps going alot further than the screw length it means the wood is rotted...
All three of my boats have the 3.0 all from the 1980's. They are still going strong. Fresh water boats last a long time. Well not so much the boat, but the motors do if taken care of. One I call my beater boat, I'm not real nice to, but it keeps on going.
Did you actually install a carb kit? And adjust the float height/drop? If all you are doing is cleaning it, it'll never be right without a new needle/seat. That bottom gasket is easily obtainable from your local parts store.
Had a similar thing on a mercruiser. It would thump no matter what gear or neutral. Alignment was good, u-joints and gimble replaced, even tried two other drives. The problem continued. We were the third shop to look it over. I moved on to a different job so I'm not sure where the issue was, but...
Pull the drive, pressure and vaccume check it. Many times its the shift shaft seal thats leaking, hopefully its that wich is an easy fix. You will have to split the drive to replace that seal.
Did you just remove the lower half? Usually removing the entire drive is easier. You have to put the shifter in to full forward to remove and replace the drive. The shoe in your pic isn't straight forward, so that might be your issue.
I use coarse/medium/fine stones in that order depending on how dull the blade is. Freehand. I only use water on the stones, when done let them dry and put away. I prefer water as its readily available and when out hunting I keep at least the fine stone in my backpack for touch ups if needed...
There are wiring codes for marine use. But if someone has been in there before, wich usually is the case, nothing will match up to the codes. Here's one example.
Marine Wire & Terminal Tech Specs | Boat wiring, Boat, Color coding (pinterest.com)