The front input has analog pre-emphasis while software provides digital de-emphasis for noise reduction (when the I/O is set to front), and it is more forgiving of overloads and soft-limits the signal to some degree. The rear has neither of these so it's flat (when the I/O is set to rear and you're plugged into the rear input), but clips harshly if overloaded.
On my personal Ultra myself and the audio pro's I work with can hear the difference between the two input methods, and we find a more natural sound for recording clean tones via the rear input (set to rear, while being very careful not to clip it!). For live use and recorded distorted tones the differences are mostly lost in the general muck.
Jay Mitchell plotted these two response curves on his personal Standard and the front (set to front) showed maybe a db of high-mid rolloff which is audible in my book with bright guitars, though not in his (he has a locked thread somewhere with his Axe's freq plots, do a search?). It also has to be noted that analog components can differ from their rated values so minor machine to machine variances are to be expected as well.
To sum up my experiences related to my personal Axe only, the front works fine for gain tones, but the rear can sound more natural for clean to edge of breakup type tones depending on a number of variables including but not limited to the guitar, pups, strings, and the individual Axe and it's settings that you're using. Personally I don't worry about it for live use and I just use the front input set to front, though for recording I'll use the rear for cleaner sounds (and line-level re-amping etc, being careful not to clip it).
Not sure of the best method of removing the analog stuff in front, and I'd venture that it wouldn't that easy (surface mount components etc), so if you really want to use the rear I'd just use an external preamp into the back there by not tearing up your Axe.
Good luck...
Thank´s for the answer !
I´m still a little confused about the differences in sound .You are saying "basically linear" ..... hmmmm
I always put a boss tuner in front of the ultra . This should mean that the impedance of any
input wouldn´t matter . I really like the sound of input 2 better ,however it´s not easy to route everything that way .
Also ,I have no problem with feeding the converter on input 2 with maximum level even though it´s a "line level" input , weird isn´t it .
If I wanted this "analog filter circuit" removed , would it be hard (cutting or shorting a cap..) ?
Thomas