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Be aware that a UV filter is not likely to be waterproof. You're going to need to pack the case with silica gel bags to prevent moisture build up. YOu also need to have the case mounted high up to avoid getting the lens coated with crud thrown up by raindrops, and you need a hood over the lens to shield it from rain and direct sunlight as much as possible. When I ran a long duration time lapse, the biggest problem I ran into was shutter failure. Work out how many shots total you;ll be taking, and see if this is more than the camera is rated for. Exposure is very important too. Do you let the camera decide on exposure, or do you set it to a constant value? Don't forget also that post processing thousands of images into a movie can be very challenging. You might want to think about adding a solar panel to keep the batteries charged (camera and intervalometer) though this will need some knowledge of electronics, as you'll need a lead acid battery to hold the charge, and a couple of voltage regulators to power the gear.
UV filters aren't designed to be waterproof. Splash resistant maybe. It may well be good enough for your purposes, but it's not going to be as well sealed as your Peli case. For suggestions on exposure and timelapse photography, there's a lot of useful information to be had here: http://lrtimelapse.com/tutorial/
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