Recheck DC volts at PI tube pins 1,3,6, and 8.
As Enzo said, if it was one of the resistors, there should be no voltage at the plate.  But might as well check their resistance, there are 3 of them: R50, R51, & R52.

 Check AC volts from orange to red of secondary, should read same as orange to black.
  Then, with power off and caps drained, check resistance of orange to red and orange to black.  Also check resistance from either heater green to ground.

  On the orange wire you are looking for AC, not DC.  Check orange to ground and also check orange to black of secondary.
  It's possible the orange is a CT of HV winding that is not used in this amp.

The brown bias winding could be bad, or may not have provided enough bias range, so someone put in an alternate bias circuit, leave it for now.

  Sounds like V3A is not conducting.  Are both sides of V3 heaters lit?  Have you resoldered that socket?  Or tried another tube there?

 Do not rewire to match the other amp.  As you can see, it has a different PT with different color wires.  And the picture Dr.Gonz posted was an example from another model so those colors don't match either.
  Have you checked that there is nothing connected to the underside of any turrets?
You have heater voltage, otherwise the tubes would not light up.  You have to measure it across the 2 green wires, not to ground.  They may be using resistors to ground from each side of the heater winding rather than a center-tap, check that there is around 6.3VAC between the heater greens and forget about it for now.
  The bias winding of the PT likely fried.  That may be why the brown is disconnected and the other bias circuit has been connected to the bridge.
  Do you measure any AC voltage from the disconnected brown or orange to ground?

  You should probably start by cleaning all the pots.  Dirt/oxidization could cause the tone control issues and the volume bleed issue.

schematic:

  So the crackling is there at any volume level if the saturation is up, but there is no crackling when the saturation pot is turned all the way down, no matter the volume level?
  If this is the case, then a dirty/oxidized  saturation control is a good bet.

  Looking a bit more, one of the taps connected to the voltage selector should also go to the pilot light.  Is that where the grn/yellow connected to the red is going?  I think the red is the 245V tap and the grn/yl it connects to should go to the pilot lamp.

Do not trust any wire colors, someone has rewired this amp using AC cord.  Does the 3rd prong on the AC plug (round pin) connect to a wire that goes to the chassis?

  Sorry I can not look at 100's of megs worth of pictures as I don't have unlimited high speed internet.
  If you are unable to read schematics you should not be doing this.
If you are able, then you should be able to follow the drawing.
Try to tell us exactly where wires are going, rather than telling what colors, the color scheme of this wiring is horrible.
  If the yellow of the PT primary is the 115V tap, then you want to connect the "out" of the fuse holder directly to the 115V tap, bypassing the voltage selector.

The only wire on the PT primary that should go to chassis is the core/case wire.  Look on the schematic at the middle of the PT, at the bottom it shows a wire going over to chassis ground.  Is the green/yellow (safety) you mentioned connected to chassis? 
Disconnect the red wire and measure the resistance to the case of the PT, does it measure as a short (0 ohms) ?

  Did you try cleaning the Sat pot?

JWOPT1 on page 1 and JWOPT2 on page 2 are definitely options that are in  place depending on whether the amp is the combo or head version.
However, the straight line short between the speaker leads (pg2, between bottom of C26 and left side of OPT2) is some kind of typo.
  If it even exists, it should be drawn as another optional jumper.

  Regarding the output tubes bias and balance, there is no adjustment, but there are specs in the notes on the schematic regarding the range of acceptable values for Vi and Vk.  If the tubes are not within the spec you replace them.

  Sounds like a bad filter cap, especially seeing as you have 363V B+ instead of 525V.
Check what the AC voltage is on the B+. (some meters will not be able to measure this properly).

  The voltage selector is a 2 piece switch, like the old style Marshall switches.  The piece you are missing looks like this:
http://www.mojotone.com/amp-parts?search=Switches+Marshall+Old+Style+Impedance+Selector+Switch
http://www.amplifiedparts.com/products/P-H502
  It will be very easy to bypass, but as Dr.Gonz stated, you need to post some pictures where we can see everything at once, not just little bits at a time.