My follow up question would be, would those lengths of connecting ground wire potentially make a significant difference to the noise floor?
No, I don't think there very long. Fender had longer runs than those. But that's not the thing.
If I've understood correctly, it would be better to attach the negative side of the filter cap to the closest ground to the tube socket and use longer lengths of wire to connect the positive side of the filter caps back to the rectifier?
That's not it either.
Each filter cap's ground lead goes to the grounds of the tube circuit that cap feeds. So node D's cap's ground lead should go to the 1st preamp tubes grounds. That will make a ground star. Then you run a wire (ground buss wire) from that ground star to the next ground star. It's a bussed multi local ground star system. It's wired ground not a random chassis ground.
You have fixed this but, you had the OT's secondary ground grounded to the 1st preamp tubes B+ node D filter cap ground. That OT ground has a lot of current, the 1st preamp tube ground star has the least current in the amp. That OT current can modulate the preamp tubes ground, that will cause humm.
So we keep the filter cap ground lead wired to the circuit grounds of the circuit that cap powers.
You put the cap close so you don't end up with long wire runs all over the chassis. Big mess.
Look at the drawings I posted from Merlin. You have your grounds jumbled together, they should be organized together with the B+ nodes filter cap ground lead that feeds the circuit, local ground star, then bussed together, then grounded at only 1 chassis point.
It looks like, from your layout drawing, it's the only thing I have to go by, that the D node cap would fit nicely on the far right side with the cap ground lead facing up towards the top of the chassis/input jack, which is where the tubes and input jack grounds are. And then you could put the + lead on the terminal lug just below that preamp tube. Nice and neat.