That does sound possibly like Alternator then. Not that it's your blower fan it has nothing to do with the A/C as I blows with heat, vent, A/C...
Sorry for nit picking but when trying to diagnose over the internet....
You might have a bad battery also. Would recommend it to get tested. Your battery should be able to maintain voltage to run all the components. With Alternator drop out. My Alternator burnt out and started having some weird gauge behavior. Don't recall if any other electrics went out but belive it was isolated to the gauge cluster and possibly the radio.
2001 ZX3 Zetec - Rebuild "The TICK" (
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2004 ZX5 SVT - Restoration "Code Name Rocket" (http://www.focusfanatics.com/forum/showthread.php?t=722698&referrerid=62897)