Mustang Boards - I come seeking help

Hello.. I posted here a few times before and it was helpful.. anyway im having big issues with an 2 unknown problems

first:
I have a mild clicking sound that only appears when the car is warmed up and only when I slowly accelerate from a stop do I hear it.. once I speed up more i cant hear it and driving any time other then this slow start I do not hear the noise.. when the car idles and u give it gas in nuetral, cant hear it.. but when I push on the brake in drive an give it a touch of gas u can hear the noise clearly. people seem to think I have something loose in the interior engine, but get this.. the Ford place I took it to says that if they tear apart the engine and discover the problem to be only wear an tear an not "broken" then my extended warranty wont cover the costs and ill be forced to pay.. this seemed gay, so they suggested I take it back to where I bought it because I have only had the car for 1000 miles... (there is 49k on it.. I bought it at 48k. 2004 v6 mustang 40th anniversary addition car) since I cant get over the snowy pass to confront the place I bought it, I called an they dont seem to want to help me at all an claim the problems wernt there when i bought the car, but the ford place I took it to thinks these problems were already on the car... so... WTF am I to do.. I bought the stupid extended warranty through National Warranty and I want my car fixed!

oh.. an the 2nd problem which im not sure is related to the first or not, is that once in 4th gear.. around 37-45 MPH the car seems to have a bogging down drown sound to it...like i push the pedal an it hums to me until I speed up or slow down.... this only happens in the 4th gear of an auto tranny... so can anyone help me with figuring out what this is..

thanks in advance for anyones input. Would appreciate it!