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Alright, I've had more time to fiddle around with this and I've hit a few snags along the way. I've posted what I've done to fix these small issues for those who may run into similar problems.

Mail Application Doesn't Launch
Problem: Launching the Mail application shows you a white screen and then closes.

Solution: Change the owner of /var/mobile/Library/Mail from "root" to "mobile"

Enter in Terminal: chown -R mobile /var/mobile/Library/Mail

NES, GBA, SNES, PSX Emulators cannot find Roms
Problem: Emulator cannot find Roms when launched.

Solution: Move roms to /var/mobile/Media/ROMs and change the owner of /var/mobile/Media/ROMs to "mobile." Lastly, add a ROMs symlink to /var/root/Media

Enter in Terminal: mv /var/root/Media/ROMs /var/mobile/Media/ROMs
Enter in Terminal: chown -R mobile /var/mobile/Media/ROMs
Enter in Terminal: ln -s /var/mobile/Media/ROMs /var/root/Media/ROMs

BeatPhone cannot find Samples
Problem: BeatPhone states it cannot find any samples when launched

Solution: Move /var/root/Media/BeatPhone to /var/mobile/Media/BeatPhone and change the folder owner to "mobile."

Enter in Terminal: mv /var/root/Media/BeatPhone /var/mobile/Media/BeatPhone
Enter in Terminal: chown -R mobile /var/mobile/Media/BeatPhone
Enter in Terminal: ln -s /var/mobile/Media/BeatPhone /var/root/Media/BeatPhone