Hello Kelly,
Shipping rules apply to all products equally, so if you want to give a specific product a specific shipping cost you would need to use packaging costs for that.
One way to approach that would be to assign a packaging type such as Large Box to the combo item and give that a cost of $4.00 ... then create shipping rules to handle the rest of your costs like the $3.99 for 1 item, $4.99 for 2 and so on.
The end result would be that an order of one of the combo items still totals to $7.99 ($4 for packaging plus $3.99 from your shipping rule), and it would scale to $8.99 if two items are ordered, etc.
It's hard to give the best recommendation for shipping settings on limited information though, so if you need further help you can email us at support@e-junkie.com or post here with more complete details about how all your shipping costs should work and we can give you more detailed instructions.
