It looks like you are going in the right direction. Storing the values in the extended data. I noticed in the Merchello source Rusty has put a comment about this too. So that might be a way to go.

https://github.com/Merchello/Merchello/blob/merchello-dev/src/Merchello.Web/Controllers/BasketControllerBase%7BT%7D.cs#L123

In a project I'm currently working on with Rusty (It's not based on top of FastTrack), we have some custom fields that need to get added to the basket lineitems too. We also need to adjust lineitems based on values the user selected on the product and added to cart (Stored in extendedData)

There is an event on the Basket called 'AddingItem' which we call in the AddToCart. It's called like so

        // Add an event handler to adjust the sku in instances where an optional delivery service is selected
        ((Basket)Basket).AddingItem += OnAddingBasketItem;

Where we use this to change the price of the line item based on what is stored in the extendedData. This might also be something you could use.

    /// <summary>
    /// Handles the Basket Adding event.
    /// </summary>
    /// <param name="sender">
    /// The sender.
    /// </param>
    /// <param name="e">
    /// The event arguments.
    /// </param>
    private void OnAddingBasketItem(CustomerItemCacheBase sender, NewEventArgs<ILineItem> e)
    {
        var deliveryServiceFee = e.Entity.ExtendedData.GetDeliveryServiceFee();
        // Other Code here removed for forum post
        e.Entity.Price = e.Entity.Price + deliveryServiceFee.Total();
    }

And the event handler is then removed further down the same action

        // remove the event handler.
        ((Basket)Basket).AddingItem -= OnAddingBasketItem;

Hope that helps...