Heidi, Regarding the fan noise, everyone I personally know who has a 500 (3 people!) has had fan noise and this seems very common. I have cure mine and my friends, see my post (How to fix a squeaky fan) or ticking for that matter. The problem seems to be a lack of lubrication but FIAT technicians just replace with another un-lubricated fan which will then be noisy in due course. If you are not technically minded, print out my post and take it with you to the dealer.
The breather pipe sounds like might also be a problem. I had the fume filled car experience and found the small breather pipe had snapped off the back of the air filter box (1.2). I fixed it by drilling a hole where the pipe had snapped and fitted a metal brake bleed valve in its place, now perfect and built to last.
Mark