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For various reasons my only good option for my shack location is on the 2nd story of my house.
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There is absolutely nothing wrong with a second story shack. There will be no problem achieving good grounding and bonding. Any other answer is ham mythology.
The good news is that there is walk-in attic space on either side of the room, which is at the end of structure, so bringing in cabling & ground won't be too hard. It is also right over the AC mains entrance with easy access to the AC safety ground.
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I saw your pic, it's actually a very nice spot, with windows and, I hope, a view.
I plan to install a network of 8-foot ground rods and bond them with exothermic weld kits. The soil is 'Carolina Clay' but stays moist. I have read and understood the
ARRL book on grounding and bonding.
My plan is to install a single-ground point panel where I'll bring in antenna feedlines through Morgan brand arrestors. The panel will have a copper backplane to set up grounding.
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More than adequate.
1) I will put a ground bus on the desk. What's the best conductor to use to wire it down to the panel? Seems too far for exposed copper strap.
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You really don't need to use copper strapping. It's overkill in nearly every application. All you need to use is 6AWG copper. Technically it should be solid, but stranded has always worked for me, and in my last station upgrade I even changed to a high strand count (welding cable) to make handling and routing it even easier. You can use jacketed or unjacketed wire. Remember that 6AWG stranded is the standard for utility pole lightning protection. It'll work fine for HF radio, too.
2) I plan to go from the panel to the ground network with copper strap.
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More than adequate.
3) I figure I'll use conduit that's larger than needed so I can run pre-terminated cable through if necessary.
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Smart. And it'll make pulls easier, and leave room for more.
4) How do you penetrate exterior siding with conduit and make it weathertight?
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See below...
5) Any pointers for improvements? Things that I should do on Day 1 because next year I'll regret not doing it?
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Use a
"terminal ground bar" and
"mechanical lugs" (these are just examples, they come in many flavors) for making ground connections to equipment in the shack. You can get them at your local electrical supply place. So easy and quick! Use the 6AWG stranded. I really like using the high strand count welding cable for this.
And that's exactly how you'll do it, if I understand your plan properly. I'm assuming that you'll have a KF7P or similar panel at ground level. What you need to do is put a similar panel directly above it located in front of the attic space, where the conduit from the panel punches straight back into that space. Finally, you'll have one or more conduits that go from the ground level box to the attic level box.
You can also forego the ground level box and just bring all your antenna feeds straight to the second floor. This can actually be quite convenient depending on your antenna setup.
I had a second floor shack for a few years and had zero problems. You will enjoy operating from up there instead of some dank basement or horrible outbuilding.