HELP: Rattling noise when car is cold please help

OK i have a 01 Cobra with about 45,000 miles and i do still have an extended warantee 5 yrs or 100,000 miles from now. I just got the car about a month ago and now that it is starting to get cold im hearing this noise. I only hear it when the car has been sitting for awhile and the engine is cold. Its like a rattling or taping kind of noise and it only happens for like 2 sec. , when u start it up. But say u only let it run for a min or two and drive it and u bring the rpm's up past 2500 it will start making the sound again. But if the car is fully warmed up to operating temp. it will not make the sound anymore. It sounds like its coming from the engine compartment. The only mods to this car are a b&m ripper shifter and a flowmaster catback. And i also have one more question when the car is warmed up to operating temp. but it is not driven and the trans isint warmed up. For like the few couple of shifts from 1st to 2nd it grinds and goes in hard, unless i shift really slow and then it wont do it. I have ideas on what it could be but this is the first ford i have ever owned and im not too fimiliar with these 4.6 cobra motors. Any help is greatly appreciated i really wanna get this taken care of as soon as i can.

Im not sure i have only had the car for like 400 miles and the oil was changed by the dealership im guessing it has 5w-30 since thats what it says right on the oil filer cap, but who knows. Now should i be concerned about this? And it makes the sound still while the motor is cold but not driving it right after starting it. I always let it run atleast a min before i drive it. And it makes that sound when it is brought roughly past 2500 rpms. Wouldent the oil be all circulated by then or is it just still too thick?

Thanks alot for ur help COBRA90GT.

cool thanks alot for the help i really appreciate it. And ur right i looked at the cap wrong it is 5w 20 and that what i think im going to do tommaro is change the oil myself at home i never take it to thoes oil change places its just that the dealership did it right before i bought the car and i didnt see a point to changing it right away. actully maybe u can awnser one more of my questions. I actully got a leak of some kind i can see some sort of buildup right on the crank pully on the inside edge, i thought it was oil but it dosent smell like it. it seems to me like power steering fluid. im going to take it in to the dealership but is that possible.

ALRIGHT thanks alot ill just have them take care of it hopefully, if not ill just bring it back. thanks again