If I remember correctly from upgrading my speakers to components, the signal goes to the tweeters first. Then you’ll see a set of wires coming out of tweeter and back down the door to the woofer.
Try connecting from where the source enters the tweeter to the new 6x9s. You can use an adapter like this if necessary.
Metra 72-8104 Speaker Wiring Harnesses For select 1992-up Toyota-built vehicles — adapt new speakers to the factory wiring plugs at Crutchfield
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