Setting up freight delivery payment process

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I have a store I'm trying to set up that has three warehouses, Claymont, DE, Clearwater, FL, and Anaheim, CA. Some of our products are very large or high quantity and require custom shipping quotes. Some of our products are actual trailers and box trucks that are turn-key ready for clients to buy in custom packages that have to be custom delivered so I was looking into purchase order options that can be manually fulfilled by a person in the shop, but still deliver the customer an estimated quote. I need a payment gateway that allows us to calculate shipping costs and then send a final invoice. 


Needs to be pretty much how the checkout is for this site: (Not sure if it will work unless there is something in the cart)


We have items that are either bought in bulk or package products. 


Is it easier to set them up individually and let the shipping calculator build an estimate based on quantity? I am afraid this may scare customers because we will occasionally get a less expensive price after we include this product on a pallet with other products ordered.


Is there a way to walk a customer through or set up an order for a customer and then let them complete the checkout? Maybe save a search or a couple carts that the customer can choose from?


Thank you in advance for any help with this. We are also probably not opposed to hiring a Shopify expert, but have not done that before so if you know of any good references that would be awesome!


Thank You