Finally, we didn't talk about the mic position. Don't forget that sound follows the inverse square law. If the mic is 18 inches from your guitar, try moving it to 9 inches--and, once you've adjusted the levels, you should find any room noise is only a quarter what it used to be.
^^This. I was going to say try moving the mic to within 3" of the neck of the guitar where neck and box of the guitar meet - and see if it sounds better. I like the sound of a very close mic'd acoustic - but especially if you're having issues with potential noise (assuming it's not your mic pre or system producing the noise).
edit: I read rest of thread and just realized you have hardware issues. Even when that is sorted- try closer mic to allow lower preamp level and see if it helps