TL;DR - The spot where my NMO ham radio antenna mount punches through the roof has been rusting for years. I think this was due to poor design of my original antenna. I've cleaned up and repainted the roof, and I think the antenna I use now will not cause the same problem again.

"Factory"-ish.
When I first installed my ham radio, I cringed at drilling a hole in my roof. In reality, that process went much more smoothly than I expected, and I was thrilled to have my Diamond antenna pushing out APRS beacons and receiving communications from my buddies on the trail.
The problem with the Diamond antenna was twofold:
- It was three feet tall and got caught on trees a lot. Sometimes it would get so caught - or hit such a big branch - that it would actually push the antenna far enough back to bend the sheet metal of the roof. It was never bad enough to tear any of the metal or rip the antenna out, but that bending did a couple things:
- Compromised the paint, which doesn't bend in the same way that metal bends
- Resulted the sheet metal no longer being completely smooth, thereby rendering the rubber gasket seal on the bottom of the NMO roof mount, less useful.
- The threaded portion of the antenna that screwed onto the NMO base was too deep. This meant that when the antenna was fully tightened, the edge would extend down past the mount and into the paint on the roof, compromising it. This was made worse when the antenna would catch on a tree, as it would then press one side of the metal antenna even harder into the paint/roof. I fixed this, but not before it was already too late.
I eventually addressed both of these issues by switching to an STI-CO antenna, but the damage was already done. That was five years ago, and the rust situation on the roof has only gotten worse in that time.

Ignore the dirty roof; it's the rust that's concerning.
I decided it was finally time to address the issue, which meant removing the NMO mount, cleaning up the rust, and protecting the area with some paint. Not hard, but inconvenient, since the "easy" way to access the NMO mount is to take out the headliner ... which requires removal of the entire interior of the cab, including the new house electrical system I recently installed.
The other option is to go in through the sunroof opening, so I decided to give that a shot in the hopes that it would save me more than a day of work!

Hope this works.
After reaching between the headliner and roof, I realized that when I'd sound deadened the cab, I'd put the sound deadening material right over the interior half of the NMO mount, which was about to be very lucky or the dumbest thing I'd ever done.

By some miracle, it turned out to be lucky. With the sticky sound deadening material holding the lower half of the mount from spinning inside the cab, I was able to unscrew the outer portion of the mount from the top in order to access the rusty roof underneath.
And then, it was time to get out the angle grinder and a flap disc.

Some very careful flap disc work left me with a big circle-ish area that was no longer rusty. Mostly.
With the rust gone, it was time for paint. I'm definitely no painter, and the black patches - usually unnoticeable, given the layers of dirt and thousands of pinstripes - sprinkled around several panels of the green Tacoma are proof of that fact.

First, primer.

Then, the only color I have around. Flat black.
I wouldn't say it came out great, but it is - for the time being anyway - less rusty. And, it's on the top of Tacoma, where only the tallest of people - and me, every time I put away the tent - will stand any sort of chance at seeing it. One thing is for sure, I will only be running the super flexible STI-CO antenna from now on, so that should any tree branches reach down to bash the antenna, it will just flippity-flop around instead of bending the roof into a waffle.

If it doesn't rust, it's perfect.
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