Take a look at the original sentence again:
Mark searched the nearly empty refrigerator for a midnight
snack his only choices were curdled milk,
stale pizza, and grape jelly, any combination of which he couldn't stomach.
You chose to fix it the correct way:
Mark searched the nearly empty refrigerator for a midnight
snack, but his only choices were curdled
milk, stale pizza, and grape jelly, any combination of which he couldn't
stomach.
Mark searched the nearly empty refrigerator for a midnight snack is a main clause. His only choices were curdled milk, stale pizza, and grape jelly is the second main clause. Using a comma and a coordinating conjunction like but is always a good option for fixing a fused sentence.