You hardware setup should be fine. Audacity is also fine. Your choice of recording software is not critical because the software simply captures the digital audio stream and writes it to your hard drive.
A “competitor” to ClickRepair is [u]Wave Corrector[/u], which is now FREE!
I’ve also had good luck with [u]Wave Repair[/u] ($30 USD). It only “touches” the audio where you identify a defect but that means it’s VERY time consuming. It usually takes me a full weekend to clean-up a digitized vinyl recording, so it wouldn’t be practical for 100 records unless they are mostly in perfect condition.
Audacity also has a Click Removal and Repair effects, or as a last resort you can zoom-in and re-draw the waveform.
You can also try some “regular” Audacity Noise Reduction but be sure to listen carefully because there can be side effects and sometimes “the cure is worse than the disease”. I’ll usually apply Noise Reduction only to the fade-ins and fade-outs. And of course, you can completely mute the silence between tracks. Or, if you are making individual tracks you can simply chop-off the lead-in lead-out gaps between songs.
I usually join both sides together and process the album as a whole.
Besides de-clicking and noise reduction, some older records are a little “dull sounding” so I’ll boost the highs with EQ (may +3 to +6dB), but that’s probably not necessary with your 90’s records.
As the last step, I’ll Normalize (AKA “maximize”) the volume. If the levels are low, that will bring them up. Or, if the processing (usually EQ) has pushed the peaks over 0dB, normalizing will bring the peaks down to 0dB to prevent clipping (distortion). Normalize before exporting to WAV or FLAC because although Audacity can go over 0dB, most file formats will clip at 0dB. (Note that normalization doesn’t match the perceived volume of different tracks.) I’ll normalize the album as a whole to maintain the original loud/soft differences between tracks, but if are always playing individual songs you can normalize the tracks individually.
The downside to WAV (besides larger files) is that metadata (tagging) is not well-supported. Your DJ/player software might not see the artist/title/album/artwork information. (Audacity can’t add the artwork. I use MP3tag, which also works with FLAC and most other formats.
And, if you are really picky about sound quality, buy the CD (or MP3/AAC)!