Jeff

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Long story short, I'm trying to figure out why the metal AC box
functions just fine for a smaller magmount, but not the larger one.

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One possible explanation is that it isn't the AC's box that's
different, but the amount of capacitive coupling furnished by
the
larger magnet mount. One way of finding out is by extending the
length of the antenna slightly to compensate for the greater
coupling.
If that lowers the SWR to a reasonable level (or even if it
doesn't, but
does lower the SWR), then you know you're onto something and can
'fiddle' with it till it's 'right'.
'Doc