Based upon reading the MS article on parallel installation I think your only installation issue might be the drive by wire. If you use a volt meter to measure the output voltage on the gas pedal / throttle box used on the 2003 hemi and confirm that at closed throttle position it measures near 0 volts and at WOT it measures near 5 volts you can probably get it to work.
My only concern might be if the computer in some situations closes the throttle plates in response to some situations even though you are pressing on the throttle. Thus, you could end up in a situation in which the Mopar computer is closing the throttle plate, while the MS3 computer thinks the throttle is WOT and pouring in more fuel.
If this occurs frequently you would then be forced to ditch the drive by wire and go with a cable operated throttle body. Of course by your post, it appears you've already figured that out.
Regards,
Joe Dokes
