It sounds as if your exhaust tappet clearance is about 0.009", which is minimum specification, and your inlet tappet clearance is about 0.003", which is some way less than minimum specification. I see no need to change the exhaust clearance, and no urgent need to attend to the inlet clearance. I agree that the best thing to do next, is to give that engine some work: run it under at least moderate load - say some fairly thick grass at least 6" high, covering a sizable area so it can work steadily for 20 minutes or more. Then let's talk about what you find while running it.
