Removing clicks/pops

First off, you are certainly going to lose quality by selecting the entire waveform and running a click/pop filter on it. I recommend you run through the entire waveform manually, work your way through 10 seconds at a time and fix any clicks/pops my manually selecting them. However, if you still feel like selecting the entire waveform, be my guest, but you're not going to be able to fix those clicks/pops that are dug in pretty good, at least not without losing quality or dealing with them only (and not the entire wave).

Since you're running Adobe Audition 1.5 and I myself use it for editing reasons, I can recommend quite a few things to work around clicks and pops. I've ran into them a countless number of times and each instance has been quite unique.

Alright, you need to determine whether you're dealing with a click (i.e. the waveform takes a huge leap for a ms, clearly visible) or if you're dealing with a brief moment of silence. Both can clearly be heard, but are sometimes indistinguishable unless you are able to visualise the problem.

If you're dealing with silence, there are two possibilities (to my knowledge) -
1) The sound has skipped (i.e. lagged) in which case you would be able to merge the wave by removing the silence manually. This requires a great deal of testing and accuracy.
2) The sound has not been recorded. This would require a re-recording and can't really be remedied, as far as I know.

However, since your main problem seems to be clicks, let's try and configure your Click/Pop Eliminator. You can access it by clicking the Effects tab -> Noise Reduction -> Click/Pop Eliminator. At first, this might seem rather complicated, but you'll get the hang of it pretty soon. Let's break it down;

The AUTO FIND ALL LEVELS setting
If you're lazy and you want to take your chances, you can always hit the Auto Find All Levels button. The filter will then find representation samples throughout the highlighted portion of your waveform and shortly after that, it will gather click-data for low, low-mid, mid, mid-high and high levels. Now, you also have two boxes where you can enter numeric values; Sensitivity and Discrimination. These are very important when dealing with the Auto Find All Levels feature.

The ranges vary from 4-50 for Sensitivity and 2-100 for Discrimination. What do they mean? Well, the lower the sensitivity is, the more clicks are likely to be found and the lower the discriminiation is, the more clicks will be fixed. So, your first shot at fixing clicks might be using this feature. Enter a setting, for instance 10-10 in both and hit the Auto Find All Levels button. Then hit OK. If you can still hear a click, undo that action and lower the values. Always undo your action if it was unsuccessful. You want to preserve as much quality as possible. Every time you run the sound through a filter, you're manipulating the sound, remember that.

DEALING WITH THE CRAP MANUALLY
Moving on, there's a Find Threshold Levels Only button, which could be used in conjunction with the Auto Find feature. It scans for dB levels, so it might work if there's a high-pitched click. However, if you're up for a challenge, you can always edit the Detection and Rejection fields. You can do this after hitting the Find Threshold Levels Only button. Do NOT hit the Auto Find All Levels button after configuring the Detection and Rejection fields, as this will reset them all to the gathered click-data.

Detection and Rejection work the same way as Sensitivity and Discrimination. Their ranges vary however. Detection has a range of 6-60 and Rejection levels range from 1-100. As you can see, there's quite a lot of tuning to do, but it might be good if you're dealing with a click which is really hard to get rid of. Just enter the lowest possible value.

Furthemore, there's the Detect Big Pops setting, which you should enable. Lowering this setting will find more pops, but I recommend keeping it relatively high. My default setting is around 80, because I usually deal with pops manually.

Do enable Second Level Verification, Pulse Train Verification and Smooth Light Crackle. Leave the other settings disabled.

Finally, there's the primitive way of dealing with clicks, if you're able to see them clearly, you can try and lower them manually by lowering them to the level of the actual music. This might work if the filter (for whatever reason may be) fails to solve the issue. It is NOT recommended, but if you can clearly see the click, it might work.

Also, I recommend visiting this site if you're looking for valid and professional expertise; http://www.audiomastersforum.net/amforum/index.php

Jam it back in, in the dark.