The "Replay Gain" figures you're seeing (actually, I think it's "Radio Gain") are the ADJUSTMENT values calculated by the analyzation process. When Replay Gain is enabled in the DSP, MJ uses those values to adjust the volume for the track when it's played. The louder the original track, the "more negative" the adjustment should have been. The quieter the original track, the "less negative" the adjustment. Theoretically, this should make all tracks sound about the same when played. A side effect of this is that ALL tracks will sound quieter than their respective originals. The global adjustment gives you the ability to shift ALL of them closer to 0db gain.
I'd leave clip protection and the other equalizer settings OFF to minimize the overall impacts on the original music. Given that you have at least 1 track that has a -5.91 adjustment, I'd also make the global adjustment a |PLS|5db instead of a |PLS|6 so it doesn't go above 0.
If you used the diskwriter process to burn the CD, then played (or imported) the CD in MJ, those tracks should sound the same with replay gain OFF in the DSP as the original tracks with replay gain ON in the DSP. You didn't try to re-analyze the imported CD tracks did you?