I developed a plugin to handle situations like this:
http://bryanheadrick.com/downloads/woocommerce-purchase-order-payment-gateway/
The basic version simply makes a "purchase order" payment gateway available for all products, but with the advanced/custom version, you can specify that it's only available when products in a specific category are in the order.
After the order is placed, it goes to "on hold" status, and after you determine shipping and apply it to the order, you can update the order status, and click "send invoice" which sends the customer a payment link to pay via paypal or one of the other normal payment gateways.