Think of your amp as a separate preamp and power amp.
The Preamp has the guitar input as its input, and FX send as its output.
The power amp has the FX return as its input and the speaker as its output.
The preamp out and power amp in are connected internally until you patch into the FX loop. Then it separates them (more or less - some signal always bleeds from preamp out to power amp in).
So use your amp as 2 pieces: Guitar to amp input, preamp out (either FX send or direct record out) to your mixer or another amp. Ignore the power amp part of your amp for now. In fact, switch on the power amp mute. Does it still crackle? If yes, the problem is in the preamp. If no, probably power amp.
Now turn the input volume to zero, and drive the FX return with another source - iPod, a different guitar preamp, whatever. Un-mute the power amp, and put it in the conditions where you tend to hear the crackle. Do you hear it? If yes, the problem is in the power amp.
If still no crackle, it could be in the FX loop. That circuit relies on a switching jack to disconnect the preamp -> power amp connection, and it may be bad. Stick a short patch cable into FX send and FX return, shorting them tigether. Does the crackle go away?
On a different note, you may want to try your delay in the FX loop. FX send -> delay in. Delay out -> FX return. Simple.