Even if I record in Analog, I still get some crackles, but they seem less obvious than in SPDIF.
Okay, finally the SPDIF doesn't seem to be the problem? Good. I assumed that in the beginning if you remember.
I have noticed that the DI tracks sometimes clip if I hit the strings really hard.
I have noticed that they seem to appear more in my rythm playing, especially when I play heavy palm mutes and sudden dynamic changes.
How hot are the pickups you use? Try another guitar with lower output just for test reasons.
Finally: I still assume - and it has been mentioned often in this thread - that your buffer settings are not appropriate. Try to monitor yourself not going through the interface and DAW and increase the buffer significantly for test reasons.