Kevin,
The screenshots of the issues are attached. This was taken on www7.
The first screenshot shows the coupon only applying to 1 item, when it should apply to both as they are the same item, just a different variant.
The second screenshot shows the urgent problem. To recreate:
1. Add the higher priced item of a variant and apply a coupon of 50%.
2. Add the lower priced item of a variant (this is where the coupon should apply to both items)
3. Delete the higher priced item and you will see the discount from the higher priced item is still applied.
I would also recommend keeping the coupon populated in the coupon textbox if only one can be applied to the order at a time. Otherwise, a small grid of applied coupons (with the ability to remove the coupon) would work.
I was unable to test making a purchase, but it is very easy to test if the correct total amount is being transmitted to Analytics/ShareASale. Just look at the view source after completing a purchase and you can see if the right values are being passed. If a coupon is applied, it should be passing the discounted amount, not the full amount. That is on a per item basis for Analytics, and a total basis for SAS.