Review the original item:
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 could not 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 could not 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.