Motorcycle Repair: Ninja has knock, combustion chambers, ninja 600

Question
Hello Mark, and happy New year!  I was hoping you could help me with a problem I am having with my 89 ninja 600. It has a tap coming from the engine. This is not a steady tap when at idle but when you give a little throttle it becomes steady around 2500-3000 RPMs then at around 3000-3500 RPMs there is no tap. I have took the head off, My timing was off by one tooth. but I found that I had a broke valve spring on the #4 cyl. I replaced the spring, "replaced the broke spring only" set my timing and I still have a tap. I know I should have taken the head to a shop and let them fix it, but this is an older bike and don't want to put a lot of money into it. I have inner and outer springs I did not take all the springs out and inspect for damage. I pushed the valves open with my thumb and they all seemed to be tight except the one that was broken. My cams were in spec and appeared to be in good condition along with timing chain guides and sprocket. My #3 piston had marks on it 2 round circles from meeting the valves. The bottom end was changed out "with a used bottom end" before I got the bike and don't know when this happened. Any advice would be greatly appreciated.
           The frustrated do it yourselfer,
                                  Torry  

Answer
Hi Torry,

Thanks for the Blessings. God be with you.

I respect you for having confidence to make repairs yourself. That's a way to learn. I don't know a pro tech that hasn't made mistakes in their careers. Mistakes happen less frequently with experience and knowledge, but they happen. Work patiently and research the work in advance for best results.

The tapping is likely caused by excessive valve clearance. Measure valve lash with engine at room temperature to know.

You can perform a cylinder compression and leak-down tests to learn the sealing properties of the combustion chambers (condition of engine). If you need how-to on this, email me for intel. You can borrow or rent tools from local car stores such as AutoZone.

The engine may be fine with a history as described. Get the cams timed properly and check valve lash (clearance). Go from there.

My email addy is: mshively1@woh.rr.com

Respectfully,
Mark Shively