No, your garage door remote should not affect anything in the car. Even if there is a sensor in the car that can pick up the frequency of the remote (unlikely), it won't respond to the code your remote transmits. Being an older opener, it probably doesn't use rolling code technology, but certainly anything in your Lincoln would be rolling code.
I'd start with the basics: disconnect the battery when you park your car, then reconnect it in the morning. If the battery isn't dead, you know your problem is in your car and not in your battery. Then I'd just start pulling fuses.
The old method of putting a voltmeter in series with the battery won't work on most newer cars because the idle current draw is so high; there's a lot of electronics that need to be kept alive when the engine is off. But you can still put an ammeter in series with the battery (being careful to shut everything off first) and measure the current draw. If a good battery is going flat overnight, that's a draw of several amps which should be easy enough to detect.
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Today's Featured Article - Show Coverage: Godfrey, Illinois Country Days - by Cindy Ladage. Except for last fourth of July's Old Gold show in Springfield, Illinois, I don't remember when it was so hot. Nevertheless, the heat didn't keep vendors and visitors alike from enjoying the third annual Country Day's Event. Jane Elliott said the event was originally a one man show. "Barry Seiler, owner of Country Town Farm Supply store used to invite people up to the Johne Deere store. He would give hats and a free meal for everyone that brings a tractor." Elliott said while this
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