If customers will be buying only one product at a time, a workaround would be to list the variations with their own price then having the customer add each one to the cart separately.
Under a products variations list:
Blue Add $5.00
Red Add $5.00
Med Add $0
XXL Add $2.00
By selecting one variation at a time, the shopping cart displays and totals them up.
Shirt $20.00 1
Shirt: Blue Add $ 5.00 1
Shirt: XXL Add $ 2.00 1
Shipping $ 4.50
Cart Total $31.50
While this works, it is very awkward. The customer has to go back to the product for each variation they want to add. The instructions to do so are somewhat confusing.
Luckily the product we plan to sell are transmissions so it will be very unlikely the customer will order more than one at a time. Otherwise there would be a problem identifying which size belonged with which color.
If the developers would make it possible to pick more than one variation from the list at a time, instead of having separate lists, the above method would work fine.