Urgent: Spark Knock, warranty expiring

Hey all, its my first post, hoping it wouldn't be such an urgent one.

I took my 2007 mustang GT, bone stock down to the paper air filter in to get the rattling noise fixed, which was due to a plate between the transmission in the motor that rattled. I got the car back and the rattle is still there, and it is definitely a spark knock at wide open throttle. Gas is not the problem its been this way, and its more apparent when cold. I'm at 35,9XX miles and warranty it about to expire. Its at dealership now.

Has anybody had the spark knocking problem? That fades away as the motor heats up. My guess was to tell them to retard the timing by just a degree or so not to reduce performance. The mechanic said he could only retard or advance timing on the computer screen he uses, he couldn't pick by how many degrees.

I can rule out fuel filter, bad gas. Thinking maybe coil over plugs? Any help is appreciated to get my car back to me and out of the hands of the mechanic! I would prefer not to reduce timing, and essentially reduce performance, but I don't want a spark knock. Any help is appreciated.

That'd be great

Talk about the perfect excuse for prob. the best performance mod. for our cars : - ).
Did yours ping prior to a good tune/ intake combo?

Any other suggestions out there? The dealership has had my car since Wed. of last week, fixing warranty stuff, I'm def. trying to get it out of there, and any help is more then appreciated.