Welcome, my name is XXXXX XXXXX I will do my best to help you with your issue.No need to replace the plywood. You might want to use a product like Nature's Miracle to de-odorize the area, This product is great for clean ups and contains an enzyme that block the odor so dog's can't smell it either. It's available at any pet supply retailer
Will it remove the smell from the wood? Do mix with water and mop or scrub the areas?
How long should I wait before laying down the new carpet?
Yes it should remove the smell. It comes in spray bottles or in a bottle without a spray. I'd wait until the plywood is completely dry. Usually 2-3 dry (not rainy or humid) days
Use it like any spray cleaner