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The erratic readings on your electric gages when you keyed your comm
transmitter were due radiation from your antenna feedline. This, in turn,
was due to a mismatch between the feedline and the antenna (probably).

A couple of things:

http://www.aeroelectric.com has an antenna analyzer which you can rent for
a month for only $25. You can use it to test out your system and see what
the problem is.

Bill Archer makes a comm antenna which can be mounted in the baggage
compartment: The SA-006. Chief Aircraft carries them
http://www.chiefaircraft.com

And yes, your comm antenna is vertically polarized, while your nav antenna
is horizontally polarized