Jeff,
If your bike steers straight without you having to pull at the 'bars, the wheel alignment should be OK. If the mudguard pulls to one side when the stay bolts are tightened, the stays probably need tweaking. If the problem only occurs at one point, remove the stay bolt from the side that rubs, and using an adjustable wrench, try bending the end of the stay slightly towards the mudguard - when the bolt is tightened again, this will tend to spring the mudguard away from the tyre.
Regards,
Eddie.