Hey Corey, welcome back and CONGRATULATIONS!
Most of what I've seen and heard about the Blues Jr. have been tweaks and mods, and like jj said,,,check Bill M's site
And then try to incorporate these mods into your initial build,,,,,so you wont have to work backwards
My friend brought me one of these and I did the "tone stack mod" and it was an improvement over stock
One of the biggest articles over @Bill M is where he builds a "special" blues junior, and converts to 5881 output tubes (which, in my mind, means it's not really a Blues
Junior anymore

)
And that's probably what I would do too.....except then you need all new iron, etc., etc....
I personally am not a big fan of the EL84 output tube tone, and
I wouldn't start a new amp build with that plan....this guy went to a lot of trouble to take a stock amp, and then change everything about it

So I thinks it's a good idea to start fresh...
Just my 2 cents......and it might serve you well to let us know what you want to accomplish with this amp...tubenit has built and designed many great amps.....his advice is invaluable,,,,as well as all of the other opinions you'll get here....nothing beats experience
I wouldn't want to talk you out of what you want to do, but I would like you to be as informed as possible to make sure you build something that you will LOVE......many guys have built many amps only to find out that they weren't exactly what they wanted them to be.....so sad