Planet Bike Cascadia fenders include two "offset" spacers that you install on the caliper side to allow the stays to clear the calipers. Works great for my application. Here's a pic of the spacers and hardware that come with the fenders:


I've also used a thread union (from the hardware store) with a couple of washers and proper length SS bolts on SKS fenders with similar success. If you've already trimmed the ends of the stays, you'll very likely come up short, though.