Hi Jeff,
1) Yes, the GEL files and docs for this are in the MCSDK. You will find the GEL file for evmc6678l in C:\ti\mcsdk_2_01_02_06\tools\program_evm\gel and the docs for programming I2C EEPROM in C:\ti\mcsdk_2_01_02_06\tools\writer\eeprom\docs.
2) I believe the I2C EEPROM on the EVM is a 24-bit device. As long as this is also true of your custom board, the same .out and GEL files should work (NOTE: it sounds like you are already aware of needing to make changes for DDR. Those will have to made in the GEL, as well, for DDR GEL initialization). Here you can find schematic and bill of materials information for the EVM: http://www.advantech.com/Support/TI-EVM/6678le_of.aspx
3) Yes, following the README in the docs directory, you will be able to load and use the eepromwriter_evm6678l.out to the device in CCS and program the I2C EEPROM.
Hope this helps.
-Jon