I've been having some trouble with the level shifter between the SD card and the 74LS299 Shift Register.
On advice from a friend, he suggested I just route the 3.3V signal directly into the 74LS chip. Apparently, this is how it's done on the Arduino shield. I did this and it works perfectly. This mod requires 1 cut trace, and 1 jumper.
I have updated the schematic with various IC, resistor and capacitor values
It also has the mod described and shown.
I am presently working on the BIOS and a manual for this board that should include the BOM and this recent MOD.
Please find the latest schematic on the share site at: