How old is the engine? May have a bad timing chain and it jumped a tooth. Are you sure the mark on the balancer is TDC. Did you change the timing cover and now the pointer is in a different location?
Yup, or could be the old worn out plastic cam timing gear.
Oops, just saw your reply!
My '64 1/2 vert. Ordered May '64. D code 4 speed, handling package, caspian blue, accent group, Ford blue manual top.
'68 vert. driver. Owned since Apr '78. C code AT, AC, PS, P disc B, PT lime gold, standard black interior and top. NOS RF fender and left quarter.New top and folding glass.