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 wanted to fix it this way:
Mark searched the nearly empty refrigerator for a midnight
snack, so his only choices were curdled
milk, stale pizza, and grape jelly, any combination of which he couldn't
stomach.
A perfectly good way to connect two main clauses is to use a comma and a coordinating conjunction like so. However, when you use this method, you must choose a coordinating conjunction that logically joins the two clauses. In the example above, so, which means as a result, would be an illogical choice.
You might want to consult the rules for fixing comma splices and fused sentences.
Go back to the sentence to try again.