Akitio Thunder 2 Middle Connector Name?
There is a connector between PCIe and Thunderbolt circuit what is it? Can I use a extender for that will it cause any problems?
There is a standard x4 PCIe slot connector between the AKiTiO Thunderbolt board and the x16 PCIe slot board. PCIe risers or extenders of any sort are not recommended as the interconnect point has an impedance match, causing signal reflections. PCIe 2.0 runs at 5Ghz and PCIe 3.0 at 8Ghz.
If needing to fit a bigger card, consider running a naked AKiTiO (all electronics out of the chassis) or open the chassis to fit bigger cards: https://egpu.io/forums/thunderbolt-enclosures/opening-up-an-akitio-thunder2-or-thunder3/