Happens more often than you think, even to experienced engine builders. I had been building engines for years and I once somehow managed to misaligned the cam timing marks on a big-block 440 mopar. The cam timing was so retarded that it wouldn't rpm past 4,000 rpm's on a motor that had previously been red-lining at 6,500 rpm! It was a lot harder to correct that problem in a auto engine than it is to fix a like problem on a bike engine. Live and learn.
Before you take anything apart, carefully analyze what you currently have. Me, I would take the cam cover off and carefully observe the action of the #1 cylinder valves as I rotate the engine 720 degrees (two complete revolutions for a four stroke) from #1 firing TDC mark back thru to #1 firing TDC mark. At firing TDC both your valve buckets should be loose. As you rotate the engine thru about 180 degrees the exhaust valve should start to open. As you approach 360 degrees the exhaust valve should close and the intake open. As you approach 540 degrees (1 1/2 revolutions) the intake should close. As you get to 720 degrees both the valve buckets should be loose again.
If you have access to a Leak Down Tester and a source of compressed air I would do a Leak Down Check before I took the engine apart again. It will show you exactly where you are losing your compression.
Most good machine or engine building shops should have a Leak Down Tester. Or, if you know anybody in General Aviation (GA), a pilot or a mechanic with a light airplane, they will have a Leak Down Tester as it is the ONLY way that you test compression in a piston engine airplane.
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