Sometimes I get weird issues on certain LDs in my collection. On the digital audio tracks I sometimes get popping noises (I think this is typically from print source used for the film), drop-outs, crackling, and audible clipping. This only happens on some discs and not always every time. I'm thinking something in my player might slightly be out of alignment somewhere, or I have some discs with issues.
Do these kinds of issues always mean laser rot?
Case in point: A recent ebay purchase of For Your Eyes Only gave me a clean disc with good video and clear audio, but there is audible noise and possible distortion in the higher frequencies.

But the big one that first alerted me to all of this was when I popped in the THX CAV box set of Thunderball for the first time. Each side starts perfectly, but anywhere from halfway to 3/4 though a CAV side, the audio begins to distort. It gets increasingly worse until by the end of the side, the PCM audio is buried under a layer of what sounds like frying bacon. The discs look spotless and the box is in great shape so that led me to believe it was my player at fault. Immediately thereafter I had a complete loss of audio when changing sides on my DTS LD of The Shadow. It finally came back after giving my player a while to rest and cool off. Thankfully I haven't had that problem ever come back up!

I had no issues when I first bought the player 3 years ago, and was told that it had been sitting in climate controlled storage for many years. Has worked fine up until a few months ago when all the hiccups started. (Pioneer CLD-D702)

If the Analog Audio is good then the the RF level may be starting to weaken. As the RF peak to peak level starts to decrease you'll start getting the digital audio dropouts first and sometimes it completely goes out before the analog stops working. You can test this by taking the top off and adjusting up the RF level.

I don't have a remote to switch to analog audio, but on my analog only discs the player auto-switches to analog. Those playback perfectly.
How would I go about adjusting the RF level? Is this relatively easy to do?

You need to take off the top, open the tray and look for a variable resistor labeled "RF LEVEL". Try turning it clockwise first and see if that helps, cannot remember on the 702 if CW or CCW increases the RF level so if CW doesn't help try CCW.

Turning right CW increases, left CCW decreases. I fiddled about with this for about an hour or so tonight-took forever to finally find the darned thing! Turning a half turn to the right made no difference to the audio, and made the video of Thunderball get filled with snow and some multicolor artifacts. For Your Eyes Only was un-affected.
Returned to normal position and turned up a quarter turn. Thunderball had all the audio defects disappear and video looked perfect. FYEO looked fine again and the audio was better. However the clicking and popping was still present in the same places-just slightly less pronounced.
Can this just happen sometimes with certain pressings? This has only happened to me on certain discs at certain points.
Thank you for the tip on this! Now I can actually watch my THX Thunderball box set!!!!!

I have only one LD that is just hard to read and even though the video can look fine it pops and clicks. I can adjust it to quit by playing with alignments but it is really the LD pressing. I think you should just use it as is until it quits as your RF output is getting weak. Either the laser or a part in the machine but probably cheaper to replace than fix.