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 - Farming Never Left My Blood - by Stan Gordon. I was born in 1947 youngest of ten of a working farm. Our farm was located in Saskatchewan near Saskatoon. We had a mixed farm consisting of grain and dairy all done with old machinery and by hand. My dad had a tractor, a Farmall A which was used mostly to run the thrashing machine, a seed drill and for plowing. I remember locals used to help each other and threshing was done from daylight to after dark, one farm to another until all farms were done.
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