When I softmod, here are the steps I take. This is only if you are putting in a larger hard drive.
Run Krazie's and backup eeprom.
FTP Eeprom.bin to the PC.
FTP C drive to PC. In your case you can FTP E too, so you will have the game save. I have a mem card on the controller, so I don't have your issues.
Use Xboxhdm and stock C (your E drive) and Eeprom.bin to build new hard drive.
Put new HD in the Xbox and run installer again. This time, do full softmod install.
This is the safest method, as you keep your stock hard drive. If anything happens you can put it back in.
With the Eeprom.bin file, you can build a new hard drive and lock it to that Xbox. So keep a copy of it in a safe place. E-mail it to yourself if you have a cloud e-mail address like gmail.
Good luck, and if you can find a MS mem card, I would buy it and copy the game save from your modded Xbox to it. Makes life a lot easier.