This answer is not intended to be condescending, but I don't know your level of experience, so I'm going deep.

First let's tackle the input jacks.

When you say "input is connected to ground" you are simplifying too much.  It is a "switched" or "shorting" jack.  It has a connection for the SHAFT, a connection for the TIP and a connection for the shorting SWITCH.  When the jack is not used, the TIP shorts to Ground via the SWITCH in order to keep noise down. When you plug a cord in it opens the SWITCH and it no longer shorts to Ground. The SHAFT is always Grounded to complete the circuit.

The jacks have a 1 meg resistor between the TIP and Ground as a Ground-Reference for the grid of the input triodes. It is high resistance to avoid shunting the in coming signal to Ground. If the TIP lug of your jack is connected directly to Ground, you wired it wrong.

Next, schematics, layouts and "e".

First off..these are schematics for the 5E8a Tweed Twin both the Fender original and one for Weber's kit...
http://www.davidsonamp.com/sf/images/twin5e8a.gif
http://taweber.powweb.com/store/5e8a_schem.jpg

These are layouts for the 5E8a...
http://elektrotanya.com/PREVIEWS/63463243/23432455/fender/fender_twin-5e8a-layout.pdf_1.png
http://taweber.powweb.com/store/5e8a_layout.jpg
http://ceriatone.com/images/layoutPic/fenderLayout/5E8ACeriatone.jpg

There is a massive difference.  The schematic is the road map of the circuit and contains a lot more information than the layout, if modding and repairing an amp, it's always best to consult the schematic, it shows exactly how the signal travels through and you can see what each and every part does and how it is connected, plus you get voltages, etc. The layout is a construction diagram designed for reference of assembly, but layouts leave out things that are assumed the an amp builder would already know -- filament/heater wires -- filter cap hook-up, etc.

It's important to note the difference. Ceriatone only provides a layout, though you may have found the 5E8a schematic in a million places on line. So, let's look at the schematic...see that the TIP of the jack is only connected to Ground via the shorting switch (the arrow), when the plug is inserted, that connection is broken.

As for the E -- It stands for (E)arth, the word for Ground throughout much of the British (or former British) Commonwealth.  it's a Ground connection, and most transformers don't have one and if yours does not...ignore that part of the layout.

As for you issue, it can be any number of things...a dozen or so points where you are losing the signal, even a bad solder joint.  It's time to chopstick your way through the signal path and see where the issue begins.

You are completely right, and I should have studied harder before answering.

The layout is NOT wrong. But it is misleading.

It lacks a note about the wire used. Those Green wires are NOT connected to the TIP, but a shielding for that wire. Nik is using shielded coax cable for his inputs....


That's this stuff...RG-174....


So the core gets used where the normal hook-up would, the braided shield is used for just that -- shielding to reduce noise...it's not necessary, it's not what the vintage amp used, but it's becoming more common practice today, especially for long wire runs across the chassis.

So, at B, C, D, E and G...where you see the Black and Green lines split...the Black line is the core of the RG-174, the Green is the braid. You do not connect the TIP to Ground at all. You also do NOT connect the middle lug of the Treble pot to Ground...that's another braid at "B".

So the core wire goes to the TIP, the braid goes to Ground...
http://www.ampmaker.com/store/Shielded-wire-PVC.html

You only connect one end of the shield to Ground in a guitar amp, the other end gets trimmed back and covered in heat shrink so that it doesn't short. This is to avoid ground loops. So, in Ceriatone's case, they ground the end that connects to the jacks and to the Volume pot.

Nik's looks clean because he's doing this to prepare it...
http://diy-fever.com/shielded-wire/

Go back and disconnect those ground wires to the TIP  and check for an unwanted ground at "B" across the Treble and Volume pots. The shield doesn't need to be hooked up right now (or ever) -- it doesn't carry the signal, it is only there for noise reduction --so go through and remove those all grounds connect to B, C, D, E, and G and test the amp.

As for the rectifiers...they turn AC into DC.  If you are getting roughly 400VDC at the rectifier side of the Standby switch...it's probably working fine.

Background is in the visual arts -- degrees are mostly animation, but work is mostly graphic design.