don't worry about it. cleaning the intake is not that difficult. if you leave the lower intake on just be certain you do not dump too much of that stuff down in there otherwise you could hydro-lock your motor. what i did was stuff some paper towels in the lower intake and soaked them with the cleaner and let it sit for 10 minutes to loosen up the gunk. then pull them out and repeat that a few times until they're clean. the best way to do it is to take out the lower intake though. as for the warning, i'm sure that is just referring to your throttle body. the throttle body plate is teflon coated. they wear off though so if your plate is a golden color its already gone. if it's black then be careful. either way you can get in there and rub gently with a towel. just spray the towel with the cleaner and rub the inside of the throttle body with it. don't spray directly on the throttle body though. and DON'T spray the electrical connection either.
its ironic that the parts guy at a ford dealer tells you to be careful. i saw a mechanic clean an intake at the dealership. you know how they did it? they leave both the upper and lower intakes on, turn the car on, and spray the cleaner in through the throttle body until the car stalls. then they repeat the process. doesn't get much worse than that.
is the cleaner you got a foaming spray? does it kinda foam up a bit if you spray it on something? if so you've got the right one. although i know others have used different cleaners and had better luck. i used the ford cleaner and it worked just fine.
