The stuttering is caused by the X-Box waiting for the DVD drive to respond. It's not there so the requests keep timing out (while it waits you get the short freezes).
Your BIOS is preventing the system from just throwing an error code (it'd be 11 by memory) but it's not stopping the console trying to talk to the phantom drive.
I know the X2 5035 has an option to disable the DVD drive entirely. The problem is it likely isn't safe to flash while your X-Box is stuttering.
First try hooking up the remains of your Thomson drive. It might be enough to make the console work long enough to flash. If that doesn't work, perhaps you could borrow a DVD drive from a friend. Otherwise, take a read through this
and see if it helps.