If I understand you correctly you were checking for piston clearance? Regardless of cam "degree" the closest valve/ piston occurance is NOT at TDC. You need to check probably 20* or so, I.E. rotate the crank "up and over" checking as you go.
It's a sad tale, alright. You aren't the first. another thing that can cause that ---not in your case, evidently---is valve float