What are the main differences between - Intel® 82598EB 10 Gigabit Ethernet Controller & Intel® 82599EB 10 Gigabit Ethernet Controller?
You can get a quick high-level comparison of the two controllers using ark.intel.com. For a more in depth comparison, you would have to go to the datasheets. If you are interested in comparing PCIe adapters based on those controllers, then the controller datasheets are probably not the best place to get a comparison.
Also, is their a dual port CX-4 interface with 82599EB?
Are you asking whether Intel makes an adapter that is dual port CX-4 interface with 82599EB? If that is your question, then the answer is definitely no. The adapters based on the 82599 contoller are the Intel(R) Ethernet X520 series with SFP+ or the T2 with twisted-pair copper support. There is no CX4 adapter.
The only current adapter from Intel with a CX4 interface is the Intel® 10 Gigabit CX4 Dual Port Server Adapter, which is based on the 82598 controller.
Let me know if you need different information.