If you have a warrenty, take the car back immediately, don't listen to that guy, don't run it till it blows, that's ignorant as hell, besides, the less work you have done to the engine the better. Right now you know most of it is good, but ya never know who might wind up working on the car, and you may get someone who's careless and lazy ripping half your motor apart cause you destroyed it, now you have some jackass putting your engine back together. This is all my opinion, but, I just prefer to keep my engine as ford built it as long as possible, until I decide to mod, in which case I'll choose a mechanic I know I can trust.
It could be something simple. Keep in mind the reason that people say run it, is, well, hah, we all know, with a modular you can have a knock or tick for 75,000 miles and never have a problem, but then you hear a horror story of a guy with 20k blow a head gasket for no reason. IMO, these cars run to 225k easy if you don't mod, and let the car warm up before crossing 2500rpm, and when I saw warm up, I mean, summer time too. I hate seeing people fire it up, pull out and start driving.... Idiots, there's little oil where it needs to be, and temperatures are sparatic, as the engine runs all parts become oiled and share heat, less expansion, also good for gaskets.
Anyways if you have a warrenty, take it to them and let "them" decide what to do. If it's your only car, you can find rentals for dirt cheap, or maybe they can give you a loaner. It sucks only having one car, I went 4 years that way, no more, I got a '97 Explorer sport 4x4, and I'll never sell it!!!!!!!