I do the same thing on my store. We have odd shaped stuff and depending on the combination of products, can save on shipping by combining things in boxes.
I setup one custom shipping module (copied the flat rate module) and made it inform the customer that shipping would be calculated manually and confirmed via email. Customers can choose a payment method on the site, but it is not configured to actually do anything automatically. After I get their email confirmation/agreement to the shipping costs, I process their payment manually.
I use a combo of Edit Orders mod and Super Orders to edit their orders once shipping costs are calculated. Because I can't edit the Shipping cost as such, I've created a 'Shipping Costs' product (invisible on the online store) that I can add to each order, edit the amount and then get the order to show the true total costs.
It's not great, but it's the only way I've figured out to get it done. What I wish I could do was to simply edit the shipping costs and have them appear as the actual shipping costs, and not have to add them as products. The show up on the packing slip and look stupid.:yuck:
The Edit Orders mod is particularly unsupported and finicky, so I feel fortunate that I have it working at all. A way to edit order contents, including attributes, that is a built-in feature of ZenCart would be awesome. :bigups: