Since you said have a copy of your stock HDD on your PC, did you put a larger HDD in your XBox, or is the stock HDD still in your XBox?
If you have a larger HDD in your XBox, I would look around on here in the B/S/T Forum and try to find an unlocked stock HDD to put back into your XBox. Once you install it, lock it you your XBox (you may need to make an EvoX boot disc with lock/unlock commands if you don't have an auto installer such as Slayers to help you with the locking part). Then delete the contents of the C:/ partition and FTP over your orginal HDD files. Once finished, reboot the XBox to make sure it is working properly. If it is, it will boot to the original MS Dashboard (even though the matrix modchip is still installed) because it is the only dashboard available. Remember to LOCK the HDD to your XBox. Now remove your Matrix chip and your XBox is now back to retail condition.
If you have the stock hdd in you XBox, simply delete the contents of the C:/ partition, FTP your original XBox HDD files back to the HDD, and LOCK the HDD. Reboot the Xbox to make sure it is working properly. Same as above; if it is, it will boot to the original MS Dashboard (even though the matrix modchip is still installed) because it is the only dashboard available. At this point you can take your Matrix chip out, and your XBox is like it was the day you bought it.