For a crackling noise the first thing I'd do is cycle the cord connections a few times to make sure the contacts are clean at the jacks and plugs.
Then I'd pull and re insert each tube just to make sure those contacts were clean.
If that didn't get rid of the crackling noise... I do a quick swap test with the phase driver/splitter/inverter tube... as a breakdown in that tube (one of the few tube positions where tube actually seems to wear out) can cause a crackling sound.
On the Hot Rod Deluxe this tube will be labeled V3.
If that doesn't help then I'd want to get more specific about what the word "crackling" is describing.
One possible clue is the "overdrive" channel. This might suggest that the problem is in the overdrive circuit... or it may suggest that the problem manifests itself when the overdrive causes extra vibration in the amp chassis and is in the general circuit.
Crackling is usually something simple... but it can be hard to locate.
best regards,
mike