I am inclined to believe one of two things;
- your bike has an actual problem of sorts
- or you are trying to ride over massive speed bumps that might bottom out most bikes
Something like a Ninja 300 should have no trouble running over 99% of speed bumps. It is not a hardcore race bike, it should have plenty of ground clearance for 99% of riders in 99% of conditions. And on top of that, you're only 187lbs, this is totally reasonable and there should be no issues in regards to your bike's suspension.
Going in and changing linkages, fork tube height, or anything else is risky if you are not very much so in tune with the trade-offs that happen when you make these changes. Handling and ergonomics will be affected, and if you are not ready for all those changes, they may be unwelcome changes.
I think after seeing your updates on this issue that you should see if the shock and fork springs are the correct rate for your weight, or if there is any malfunctions with the shock or forks. I am 150lbs, and the stock fork and shock springs are just adequate for me, at a medium/advanced track pace. But I have maxed out the preload on the rear shock, and I think everyone should do that if you have the stock shock.
Make sure your suspension isn't binding. If it is binding, then it may 'stick' and be stuck down low like you are experiencing. I have experienced this, it happened to my 300 because the grease in my lower suspension pivots had entirely dried up and began seizing. It made my rear end not re-extend.
All this to say, I would make sure you are 110% sure absolutely nothing is wrong with your suspension before deciding to leave the raising link on the bike. Raising the front or rear end with modifications or aftermarket parts I think would be a band-aid over the real problem.
I think there is some missing info here. Pull the bodywork off the bike and take a look, and if you have the tools, take the shock out and make sure all the swingarm pivot points move buttery smooth with no resistance without the shock in the bike.
-Mike