Thanks for your comments Jack, the torque converter especially sounds like something I should chase down.
There are several sounds I've talked about and I've taken care of or at least identified everything except for this clack which sounds like someone wailing on the valve cover with a wrench. I can barely get it to happen in park if I really rev the engine, and even then it is extremely faint. However it is very loud and certainly noticeable, almost frightening, at certain throttle settings while at speed (>=40mph). To the extent I can hear it at all with my head stuck in the engine bay in park, it sounds like it is coming from somewhere from deep within the rear of the engine, at or below cylinder #6. So that would in fact be in the general area of the torque converter.
I am going to do some more reading about the TC. In the meantime, are there any simple diagnostics that could rule it in or out? I'm guessing it only comes into play when the transmission is in gear and moving? This kind of fits with the fact that we really only hear it while driving, although as I say if I really gun it in park you can barely kind of hear it even then.
In my cursory flip through the Chilton and Haynes tonight it seems like I'd have to drop the tranny to check out the torque converter - is that about right?
In fairness of my mechanic, he actually didn't recommend an engine rebuild - when I brought it in I told him not to do anything that would rack up major labor charges. I mostly wanted to see if knowledgeable eyes could detect something obvious which I, as usual, would have overlooked or known nothing about. He didn't say the scratched cylinders were definitely the cause, just that in the amount of looking he did, that was the only thing he saw which might be problematic, and could potentially account for what we were hearing. He didn't even have the head off - he inspected the cylinders with a borescope. In the end we both remained somewhat stumped pending further searching. In my present situation I am limited to further searching that doesn't involve pulling the block, only he kind of thought pulling the engine might be the next logical step.
Gene: yes, the head leak was in fact on the driver's side, every time. It seems to have disappeared after my last re-torque.
I also do in fact have an exhaust leak between the 3&4 cylinders, I think this is due to the incomplete manner in which the port divider was welded in at the machine shop. But anyway I know about that one and it can be fixed.
Luke