Theatre Bypass Mod for CJ Preamp?

Not sure that I understand your sonic concerns.Any 1/2 decent 2 ch pre amp should KILL the sound from a proscessor's preamp.Do we have a decent 2 ch amp?/or are we using a 5ch affair? The 2 ch pre is only a 'half' of the equation;a good 2 ch amp,being the other half.
Streetman:I have a Pioneer Elete with 2 coax outs. One is for DD,DTS/it goes to the dig.in of the processor.The other is the PCM/48,and that goes to my dac input for 2 ch.

My concern is that the signal will flow through the attunator in the processor, then again through the entire gain stage of the CJ. The THX processor is decidedly leaner sounding than the CJ. The mains will have been subject to the influence of the CJ, making them different in character from the remainder of the system is theatre mode. As for amplification I am using an Adcom GFA-555 for the mains and an Adcom 2535 with two of the four channels bridged for center and rear duties. Not the world's greatest rig, but a big step from my previous one. I suppose I could re cable the center and surrounds to bring them closer to the sound of the CJ ... More resons to tweak.

Streetman - almost forgot to address your question. I recently had to do what you propose for a short time. The only link that was needed between the processor and DVD was digital. The analog outs went to the pre amp for stereo. WARNING - most mass market DVD players sound terrible for music. My wife actually begged me to put the CAL back in the system when I did this. If you have a mass market DVD do not fail to go out and buy a seperate D/A to do stereo. Even a used Theta Cobalt or CAL Sigma is a huge step up from stock DVD analog outs!!! Or go one better and pick up a used CAL Icon MkII. Cheap and good with a better transport than average DVD players.