In a 3gal tank I hope you're doing daily 50% PWC?
The more room you can give the fry and the more feedings and water changes, the faster they will grow.
If you have another tank to divide them into, I'd go ahead and do it. With that much difference in their sizes already it's likely that the larger guppies are outcompeting the smaller for food; which will just stunt their growth even further.
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