This is my first go around and your layout looked very alien to me. I was having a hard time seeing where the grounding was other than the power cord. I barely have any concept of what my layout is actually doing.
When I get a chance I'll try to re-post the 5E3 layout with the B+ ground buss colored in green for clarity.
Yes it is alien!

FWIW, IMO, for a first go round you've done great. And you're now fine tuning it and it's getting even better.

I used to think,

hum, well a ground is a ground, right? It all goes to the same place right, to ground? What's the big deal?

And it took me a while (well a LOOONNGG time, bit by bit

) also to read and study schematics and layout drawings to start to get it, most if not all will tell you the same thing.
Tim, I'm still trying to figure it out too, you'll get it, you olgoat you.

(Sorry I just could'nt resist

)
Take some time and read and then re-read and then re-re-read Merlins info, as our friend archaos posted the link earler for you (here it is again;
http://valvewizard2.webs.com/Grounding.pdf) and any other stuff you can till it makes scence to you, it's what we all do.
Bottom line is (to me anyway), it looks like your speaker jack is a metal Switchcraft type and if this is true, you don't need to run it's ground over to the main ground point, because it's _already_ grounded to/at the chassis. So nothing to worry about as far as where to rout it. Many amps including Fender grounded the OT at the speaker jack to the chassis. What the guys told you about where/how to ground the B+ filter caps is the bigger part, and you've already done that. It worked, so this is good.
Weber talk about the same B+ filter cap ground fixes for Fenders, that the guys have showed you, years ago in his books.
But I still think you should get rid of the ground wire that's running from the speaker jack (and is all tangled up with the power tube socket's wires), over to the main chassis ground point.
When you lift that ground wire, if it were me I'd lift _both ends and take it all the way out_ and then see if it makes a difference.
Gonna be a great sounding and playing amp when you're done Tim.
Brad