Take another look at the original sentence:

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.

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