Doe this mean I have no worries as I am on a modded dash?
No. You're building a new disk, start with a clean 5960 Dash.
And, for someone who is concerned about making sure he uses the most recent methods, you certainly didn't do your homework on the softmod. The tutorial you used is 18 months old, and the softmod it recommends, SID 2.0, is extremely old (2005-02-20) very buggy, and really old technology. The latest SID version is 5.01, but the best current gamesave softmod is Krayzie 1.1.1, the latest and best hotswap / ftp softmod is Kingroach NDURE 3.1.
Build your xboxhdm disc using the stock C from Slayers / AID, and Kingroach NDURE 3.1, and your eeprom.bin. Put the stock C in linux/C, and the Kingroach 3.1 files in linux/ndure (the Kingroach C and E directories and the ndure script should be immediately below this i.e. linux/ndure/C/ and linux/ndure/E/), and eeprom.bin in linux/eeprom/
Run xboxhdm, select option 1 - boot VGA Console, then type xboxhd, then select option 2 - Rebuild C partition on existing Xbox drive. Once that has finished exit, then type xbrowser, run the ndure script, then select option 1. Finally, reboot, select option 4 (Boot to Dos with HD unlock tools), and lock the disk with lockhd -a