[jocko]

concur. #1 comes to TDC twice during a 4-stroke process, compression and exhaust. #1 should be on compression stroke when setting the timing (i.e. around TDC and rotor pointing at the #1 cylinder spark plug tower - just before ignition with both valves closed). If both valves for #1 cyl are not closed (like you mention 3,5,7 are) then it's not on the compression stroke. Sounds like you may be on the exhaust stroke. Was the dot on cam timing gear at the bottommost point and the dot on the crank timing gear at the uppermost point - i.e. aligned to each other vertically - during assembly?

Personally, before tearing things apart, recommend reset TDC on #1. If it looks like the valves are closed, then set your timing and try to start it. If you reset TDC on #1 and it looks like you describe now, rotate another full rotation of the crank (this is only a 1/2 rotation of the cam gear for SA) and bring #1 back to TDC again - and confirm both #1 valves are closed - then set timing and try to start it.