[GTP Dad]

Unfortunately, it sounds like you will be redoing this job in the near future. The bolts must go in exactly the way the book says. If you do not put them in the correct locations the bolts will torque but the head will not be tight enough to prevent coolant from leaking past the head gasket and into the cylinders. As for the valves the oil may be thinning due to water contamination and causing the valves to tap. However, if the heads aren't torqued properly the lash on the valves will be off slightly and will cause the noise. As for the transmission, no idea on that one.