I am getting crackling and popping noises coming through my amplifier when my foot is actively engaged in pedaling.

You might want to check the rest point of the pot... the mechanism MAY have slipped causing this.

I have the same problem, but when I remove the metal bottom it works. When I put it back it makes noise again.

Using a common lead pencil, gently tap on the smaller tubes in the unit, listening for noises and crackling to change and the drive channel changes.

It is normal to get a slight twang when doing this from the microphonics of the tubes, however, the crackling and up and down volume points to a bad tube.

Replace the string. Possible sources are "dial cord" used in older radios to move the dial pointer... Find it online.

Another source might be braided fishing line.

With everything switched off. I will surmise that you are using the onboard battery with the foot pedal and not a power supply.
1. Plug lead from guitar/instrument into INPUT side of pedal
2. Plug lead from OUTPUT side of pedal into amplifier INPUT.
3. Turn amplifier volume to about 10 o'clock - to stop blowing your ears out.
4. Turn volume up on guitar to acceptable level.
5. press foot switch on pedal and adjust pedal controls to suit your type of distortion.
6. Play like Hendrix.
Good Luck
ps Just as an after thought rechargeable 9volt batteries are the way to go. I've been using them for years as I always get caught up in the power cable.
If you're going to add another pedal like a Phaser, Compressor, Flanger or what just use small connect leads between each pedal but always, always put the compressor pedal last in the line.

Good strings. Ernie Ball has been around for years. Not only strings but teach yourself books, scores, guitar accessories. The late Jeff Healey only used Ernie Ball Slinky Electric guitar strings. If you haven't listened to Jeff Healey and you thought Jimi Hendrix was good have a listen to this guy and remember he's blind.
Good Luck

If the footswitch is not switching correctly, open it up and check for any shorts or a defective switch. Sounds like it's a problem with the switch.

Ah yes, the Fender Hot Rod Deluxe. I have seen more of these in my shop than any other amplifier!! I have even sent recomendations for design changes to Fender about this amplifier.
Sadly, your amp tech may be correct: while the amp is within working specs, you can still have an issue with a bad socket. The cheapest thing to try is to replace the preamp tube(s) you think may be causing the problem. If the problem persists, it may need to be serviced on this issue (by a different 'certified Fender tech'). In defense of the last tech you had work on this amp, these amplifiers have a brittle design and do not gig or travel well (there are a minority of these amps made that do perform). Fender tried to do too much for the price on this model: best advice is to fix it, sell it and get your tone with a more stable model made by Fender (like the new vintage re-issues). Fender, like Marshall, has for years been having problems when they get too far from thier 'working reciepe' of what made them great companies.
You likely have a socket that needs re-tensioned, or a preamp tube not behaving. If it is not these, then a tech had to dive in the house of cards that is this circuit. Sorry for the bad news on this, but it is the truth. I only take on Hot Rods that 'appear' to be fixable. I am a development engineer, build amps from scratch and fix them for the local music shops, and my success rate is a dismal 60%-ish percent on these...
Thanks,-mike

Run a jack from your guitar to Input R Mono on the pedal.
Run a jack from Output R Mono on the pedal to the input of your amplifier.
There is a switch for guitar or Bass. Put the swich on guitar
You do not need a preamp to use this pedal.
Hope this helps,
Maxx.