You did a wholesale replacement of the ribbon cables?

My bet would be a bad solder joint somewhere - maybe yours, maybe Fender's. Or it could be those <not> wonderful PCB-mounted tube sockets. Get some contact cleaner and go to town. Then do a little re-tensioning of the tube sockets.
http://billmaudio.com/wp/?page_id=171I wouldn't touch the plate resistors unless they look burnt or measure out of spec. Hoffman's recommendations assume a vintage Fender amp with carbon comp resistors. Blues Jr. is either metal film or carbon film. Not a likely candidate for crackling.
Do you have a "known good" set of output tubes to try? Blues Jr.s are biased relatively hot from the factory, and they tend to eat EL-84 power tubes. Mine sure did. The issue actually is that the bias voltage is too low (in an absolute value sense). There needs to be a greater negative voltage to bias the output tubes more reasonably. However, the bias level itself isn't making the crackling noise. Toasted power tubes could be.
Bill Machrone is well known for his Blues Jr. mods:
http://billmaudio.com/wp/ At the risk of uttering heresy, the BillM mods point the Blues Jr. in a particular direction which you may or may not like. They seem to be very popular. However, after building a few amps and going back inside the Blues Jr. there are some mods I would try & others I would avoid. For example, a bigger output transformer is NOT necessarily better - I know from direct A/B comparisons in a Tweed Princeton build. Most of Bill's mods are geared toward more headroom and a cleaner, Blackface Fender type tone. Great sound if that's what you want, but you can point it in the direction of a Marshall 18-watt more easily IMHO. (Hint- Mark Huss's "cathode follower mod" and change the slope resistor to 56K or even 47K)
There's also the longest running thread in history over on the Fender Discussion Page:
Blues Jr. Mafia thread Glancing through recent posts, I think it was much more useful several years ago when BillM wasn't every third post.
The posts which say something along the lines of "
After I added the Mercury Magnetics transformer set, put in a _____ speaker, replaced all the tubes and filter caps, added adjustable bias, changed the topology of the tone stack, and put it in a new, bubinga cab, my Blues Jr. sounds great!" just kill me. Why not just build a decent 18-Watt Stout with reverb and have an amp that will sound great AND last a long time??? (Note: I'm not making up the "bubinga" cab. I'm not that imaginative!)
Bill's site used to include one approach to adjustable bias; however, he seems more focused on selling his kits now and I can't find the old instructions. Here's a pic of how I did it with a 2001 "green board" Blues Jr. I did a write up on the process somewhere out here on the web but can't find it now.

Replacing the crappy stock speaker was the best bang-for-the-buck upgrade I ever did... in almost anything! A nice 12AX7 in the V1 spot and Ei or EH or (anything other than Sovtek or Mesa) power tubes also does wonders to the tone.
My experience fixing things on my Blues Junior is that the amp is so poorly built, every time I fix one thing something else goes bad shortly thereafter. The board mounted input jack is a bad connection waiting to happen. The board mounted control pots are flimsy. The ribbon cables are a nightmare. Solder pads are small & fragile. Just about every component is as cheap as it can be. But hey, it was my first amp and it was cheap. Used ones are even cheaper

Hope this helps,
Chip