Can you do this, perhaps via the level select code?
Or must you complete the whole game again?
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You can get the 6 Emeralds in the first 6 Acts you play, you have in total 10 chances to get them. The important thing is that you collect them before Scrap Brain Zone, because there's no access to Special Stage there. Here is an example video:
Each zone before Scrap Brain Zone has one color of emerald. He gets the last Emerald on Star Light Zone 2, before completing Star Light Zone 3 and the whole Scrap Brain Zone.
Here's a trick I remember from my childhood that relies on the fact that you keep emeralds upon resetting the Genesis.
You'll then start the level you chose, and you'll still have all of the emeralds you acquired. This cheat guide confirms my memory.