Bill M Mods say the speaker is the last thing you need to mod on a blues JR if you do all the other mods. "The Billm basic mods will go a long way to helping this speaker deliver." This webpage goes over all of the speakers and how they sound in a Blues JR.
http://billmaudio.com/wp/?page_id=295
I did almost every single mod to my green board blues jr, and thought it made a huge difference. Then I experimented with stock speaker versus eminence swamp thang versus governor. I think swamp thang sounded the cleanest, sort of wish I still had it in my bluesJR, but am happy with the governor 
Here's an excerpt of the page linked above:
Fender Special Design (stock speaker)
This is the stock speaker in all black and blonde Tolex Blues Juniors and old green board tweeds. The speaker is made by Eminence and it’s roughly equivalent to the Legend 125/1258. This speaker has been used in hundreds of thousands of Fender amps, including the Deluxe Reverb, Hot Rod Deluxe, Twin Reverb, Blues Deluxe, and many others. It’s a decent, all-around speaker. It doesn’t have the deepest bass, and the highs can sound kind of fizzy, but it’s well balanced. Many people decide to leave it alone after they do the mods. The “farty” tone in the bass of a stock Blues Junior is mostly due to poor design decisions in the amp, not flaws in the speaker. One surprising new observation about the stock speaker: The more power you give it, the better it sounds. My 5881-powered 25-watt Blues Junior has the stock speaker in it, and it sounds awesome. The Billm basic mods will go a long way to helping this speaker deliver.
Eminence Cannabis Rex
The Cannabis Rex gets its name from its hemp cone. Hemp fibers strengthen the cone and impart a different flavor than typical paper cones. The cones are made for Eminence by Tone Tubby, the leader in hemp-cone speakers. This is the warm/clean jazz speaker! It’s a great clean speaker, but its cleans have that hemp cone personality–soft-edged, but not mushy. It handles overdrive and distortion very well when you push it. It’s very efficient, one of the loudest speakers you can put in an amp, and it pushes out pretty, round bass notes really well. The top end is very sweet, even forgiving. This speaker couldn’t make a harsh note if it tried and is beautifully balanced bottom to top. Super for creamy lead work.
Eminence Swamp Thang
There’s nothing swampy about the Swamp Thang–this is the loudest, cleanest speaker in Eminence’s lineup, but its response is tilted towards the bass side. Eminence calls the treble response moderate, but I find its highs more prominent than the Texas Heat’s. It produces big, round lows, even in the BJr’s small cabinet. The magnet is huge and it will add noticeable weight to your BJr. It might hit an aftermarket, larger output transformer like the Heyboer I use. You can probably spin the baffle 180 degrees to place it at the lower right instead of upper left (from the back) for clearance. I use the Swamp Thang on my test bench because it’s so clean (I want to hear the amp, not the speaker) and the moderate highs keep the ice pick tones out of my ears. The Swamp Thang is not a truly neutral speaker; it adds a warm, woodwind-like undertone.
Celestion Vintage 30
The V30 was one of the tone pillars of the classic rock era: huge, powerful mids and early breakup. Four of these in a half stack and you were on your way to rock god status. But they were often tempered in half stacks by a pair of Greenbacks to fill out the bottom end. The V30 has less bass and less treble than the stock Special Design speaker. Fender chose the V30 for the Texas Red special edition of the Blues Junior and you can hear the difference right away. It’s a standout for lead guitar and for rhythm guitar that stays out of the way of the bass player. If you like thumpy bass or need clean headroom, look elsewhere. Some players say they get more clean headroom with the V30, but I think that’s because the mids are prominent and that’s the most sensitive area of our hearing, so it sounds louder.
- Nic from Detroit...
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