Yellows..(2) rectifier pins 2/8
yep (and the B+ is taken from pin 8 as well, and goes to the +ve side of the reservoir (1st) filter cap).
Reds...(2) rectifier pins 4/6
yep
Greens..(2) pilot/heaters
yep. You can either use the green/white heater winding CT (OR you can make an artificial ground reference with 2 x 100R resistors, one from each side of the heater winding, each going) to ground with the power amp ground returns (BUT do not use both methods at the same time - just use one way or the other).
For an elevated heater - put this preferred ground return point to pin 8 of one of the 6V6 sockets (alongside the cathode resistor ;-) - this will elevate the heater winding to the same voltage as the 6V6 cathodes, which eliminates any source of heater hum noise getting into the pre-amp signal.
Blacks..(2) power and common
yep. Put the Mains fuse on the active/phase side (and then the mains switch, and then the PT primary). With the fuse holder, remember to wire the mains/hot side of the phase/active wire to the tip-end of the fuse holder (and not the sleeve end) in order to save accidental electrocution if you have the fuse cap off.
Red w/ yellow to cathode
Nope - red-yellow is the HT centre tap, and ideally that goes to exactly the same ground return pint as your reservoir filter cap ground return for quietest operation. See R.G. Keen's article (attached)
The questions.. No use and tape off separately???
Orange, green w/white (6.3v center tap), Red w/green (bias)
See my earlier comment about the heater CT. You don't need the (red/green) bias tap in the 5E3, so put some heat-shrink over the bare end and tuck it away where its not going to short onto anything/the chassis.