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I have a 1999 Civic EX and I am installing a Pioneer DEH-3300ub head unit this weekend. I was checking out the harness and had a wiring question..Setting aside all the speaker wires,
and looking at this picture i took (on white paper for contrast)

1 connects to 6 yellow yellow of course..
2 Black form radio is to be screwed to a bare metal ground? (According to the instructions with the radio) Or can i cut that wire and connect it through the harness to the 5 wire (Because I would guess that the black wire is already sufficiently grounded?)
3 Is described at "Terminal Controlled by Ignition Switch" so i want to connect that to 9 (Described as Red -12 Volts switched Power)
4 Is the auto/antenna relay control or amp (Sends a "radio is on" signal to an external device?) do I connect this to 10? Or do I leave it as is? I don't have an amp, and I have the integrated rear window antenna...
7 and 8 are the death wires and I just cap them

I have read so many head unit horror stories with the 7th gen wiring I just don't want to mess this up...thanks...
I can post more pictures during the install if people would like to see more innards of a 1999 Civic EX

Here is the wiring diagram for the adapter

 
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On the ground, I wired directly into the ground of the harness.

I agree with your take on the red wire (12v ignition switch)

On the blue wire, I would not connect it, as you don't have the device to be controlled (power antenna/amp)

On the Orange or Orange White, it appears the harness that attaches to the radio has no provision for Orange or Orange/White so there's nothing you could attach them to anyway, so don't connect it.

I don't think the wiring harness on the civic is any trickier than any other Honda. In fact, its pretty much the same deal (I think guys who buy the Civic tend to tinker more than Accord owners; different demographic).

 
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Yeah, It just seemed odd to me that you would have a grounding screw for the pioneer head unit instead of just running it through the harness to the original ground...Seems like one more pain in the *** thing to have to connect/disconnect..

 
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Just a follow up on this...I wired the reds to each other, cut the black and spliced them and did the yellow to yellow and all other matching colors. I left the blue capped and capped the orange and orange/white to isolate them...The posi products quick caps were awesome to work with

The Pioneer DEH-3300Ub works awesome. Even the stock speakers have some new life
I made a video of the whole install if anyone is interested. I just have to get it edited and Upped to youtube...

 
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I'd love to see the video. I just put a Pioneer AVIC X930BT in my 2003, and it really went in nicely. The sound is a huge improvement over the stock radio/CD