Uploaded  video no. 3 explaining the schematic overhaul, JTAG wiring (w/ a little background on JTAG - though focused on the implementation), and discussing the decoupling.  For a detailed discussion of JTAG, I suggest having a look at EEVBlog and Dave Jones' video on JTAG and Boundary Scan.  He does a great job explaining the in's and out's for the novice and the old pro alike.  

I have also uploaded detailed schematics to my repository in git.  

Next video we'll discuss the SPI multiplexing (necessary if the FPGA and Arduino are both going to master the SPI flash) and the power supply.  Also finalizing the IO and finally we'll move into layout.  Parts have been ordered and arrived today so it is moving along quickly!