I got the engine at TDC and then loosened the intake sprocket, got it lined up, then did the exhaust. Then rotated the engine and double checked it.
careful, if you are off one tooth, it will sound like what you describe, also, the flywheel has a hole on both sides. So you can have the pin inside and be 180 degrees out, ask how I know...
When doing the intake cam, if you cannot rotate it into place because it feels as though it is binding, you are a tooth off.