I already have a good setup for modding, so I don't know if it would apply to you. This is what I would do:
Since the drives are not the same size, there's not much sense in cloning it. Therefore, I would copy in my MechAssault gamesave from my memory card, and run EvoX. I'd run the backup tool and FTP the backup data (eeprom.bin, hddkey.txt, etc.) to my PC.
I have an Xbox with a flashed TSOP, so I'd put the new HD in my Xbox, and use Slayer's Auto-Installer CD to build a new large HD. After building it, I'd FTP and put in the softmod.
Then, I'd put the newly-built HD into my PC and run liveinfo to get the password, and lock it with unlockx or hdlock (sometimes only one works).
From there, I'd stick it in the new Xbox and watch it boot up in all it's modded glory.
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If I didn't have MechAssault or a memory card, then I'd probably hotswap the audio exploit and EvoX into the retail HD and run the EvoX backup tool that way.
If I didn't have a flashed Xbox, I'd unlock the retail HD and clone it to the new HD. This is much faster than cloning a 120 GB drive to it. Then, I'd lock the new HD (liveinfo, unlockx/hdlock) and boot it up. Since it's cloned, it will either have the gamesave or the audio exploit already. From there, I'd install PBL, format the F: drive, and then transfer apps to it through FTP. I'd either FTP from PC to Xbox, or I'd transfer from Xbox to Xbox using Avalaunch. I'd also lock the retail HD again and test that it works (it's a good last resort for fixing clock loops).
If I wanted to flash the TSOP instead of softmodding it, I'd solder the flash points and then use the gamesave or audio exploit (NOT the font exploit) to flash it with EvoX or raincoat. After it's flashed, I'd stick in the new drive and boot up Slayer's CD.