Speaker Issue

I have an 86 Bmw 325es with a mostly stock stereo system. I have upgraded the headunit to a Jvc unit as well as added 2 10" subwoofers in a ported box with a single amp. I switched out the rear deck speakers for a pari of Pioneer 3-way 6x9's which are the issue i am having. For everything i can tell, they are working, i can see the woofer pump with the bass, but i am getting no highs/vocals out of them at all. I tried turning the bass all the way down and got nothing. I am curious how to find out if the speakers are malfunctioning or somehting in the system is. I am still using all stock wiring from the head-unit to all speakers. WOuld my sub and amp wiring in the trunk affect how anyother part of the system worked?

Check the sound settings on the head unit first, you may have something selected which only lets bass reach the rear speakers (peek into your manual).  If that's not it, my bet is the factory 6 x 9's were only used as woofers, so you've probably got a factory amp feeding them only low signals.  To test, you can run some speaker wire directly from your deck and see if you get full range sound.

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My ex once told me I have a perfect face for radio.

I think geepherder got it right.  Most likely the rear speakers you replaced are being fed low frequencies only from the factory amplifier.  This means you will have to bypass the amplifier.