Yes, using assembly management in NAV2013 would best fit your needs. What we've done for some of our clients is creating a "kit builder" functionality. Basically, the user would select this assembly item number, then a list of options would be displayed allowing the user to select the features for your build (i.e. 1 CPU, 1 HD, etc, etc).
Without doing customization, you can manually edit the order via the assembly order on the sales order.