I put the car back together tonight. The original scraping noise apparently was coming from one of the timing belt covers. The Miata engine has 3 plastic covers over the timing belt. Interestingly enough, the top two are available on ebay while the bottom one is not. Calling the normal "Miata recycling center" was rewarded with the answer "We have one but it's pretty torn up too".
Ok, Seems to me this is a weak point is the design. Called an old friend who owns several race prepped versions he rents out for racing. He also says he's short a lower cover.
Seems the problem is that the timing marks are cast into the part and when the water pump/alternator belt breaks it tears the marks away from the rest of the cover.
OTOH, the part was only ~$40 from the dealer. Yea, pretty pricey for a piece of plastic with metal inserts but cheaper then the couple hours it would take to make a fiberglass copy. Toss in another ~$40 for replacement an upper radiator hose and belts (AC and Waterpump/Alternator). Now she's back together, but may still need a radiator tank. Seems to have a pinhole leak. But since it's a plastic tank, I'll drill it out and try a screw & gasket before spending the time & $$$ for an new one.