I think your being a little too sensitive. Especially if you came out of a 98. These engines are quiet, and they all have their own personality. All three of mine have made all sorts of strange noises, and they never let me down except when I put in a bad load of fuel in the 06. I guarantee you your 98 made all sorts of noises, but because they did not control the injection events like today, you just couldn't hear them from all the knocking. And yes that 98 knocking was caused by pistons and cylinder walls vibrating from the combustion events, and they lived on for many hundreds of thousands of trouble free miles.
If it was mine I would get it back and drive the pants off it. In all likelihood there is nothing wrong with it, and a little pinging is not going to hurt anything. When something goes wrong with one of these engines you will know it because they will knock like they ran out of oil. Just do a search and you will find very few engines that failed for any reason, especially from some minor noise.
I don't mean to sound harsh, but your just frustrating yourself by letting the dealer try and find a problem that is really insignificant.
The clutch was a known problem and they jumped on the fix for that right away. I only recall a couple of repeat clutch failures, and that was early on in the model year. Also just like your clutch did, they failed right away.