brent - plugs, wires, fuel filter
about the octane booster -- it is utter crap. they sell these bottles for like $3-4 each and they raise your octane from 87 to 87.2. that won't make a difference at all on the knock meter. octane boosters increase in tenths instead of full points.
i doubt his main bearings are going out already. he has a 2004.5 mustang and with roughly 3200mi on his car, i would certainly hope it's not the bearings.
lastly, BP - if the higher 89 octane doesnt fix it, take it back to ford. you still have a warrenty on it and it shouldnt make that noise at all. heck, you could take it back now because the v6 mustang is designed to run on 87 octane and you shouldnt have to spend $0.10 more each gallon because it is causing detonation. your call though of course