If you use SHNTOOLs, you can generate a CUE sheet of the existing Tracks, and then Join them all together. In CDWave, you can then open the entire Joined file and apply the CUE sheet. This will make sure any track marks you might want to keep remain the same, while allowing you to adjust others...
Also, you can use EAC to Extract the whole disc at once (Disc Image) or each individual track (and set it to Remove Silent Blocks). I would do each track with the Remove Silent Block checked. Its been such a long time, but I think some burning programs would correct for SBEs by filling in the missing data with silence...
I think you're just going to have to experiment to figure out what works best for you...
Terry