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 - Old Time Threshing - by Anthony West. A lovely harvest evening late September 1947, I was a school boy, like all school boys I loved harvest time. The golden corn ripens well and early, the stoking, stacking,.... the drawing in with the tractors and trailers and a few buck rakes thrown in, and possibly a heavy horse. It would be a great day for the collies and the terrier dogs, rats and mice would be at the bottom of the stacks so the dogs, would have a busy time hunting and killing, all the corn was gathered and ricked in what we c
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