There is nothing more frustrating than shooting for a full week, rapping over 800 shutter actuations, and having all kinds of wonderful plant growth just to realize you did not setup the camera properly and totally blew the shoot.
Here is my general setup. (in a nutshell, manual everything)
Aperture = Manual (normally between f/8 and f/16)
Shutter = Manual, 1.5 to 2 second shutter speed. The longer the better.
Focus = Manual. Do not use autofocus with this. Odds are it is going to screw up a shot here and there making the timelapse unusable, or at minimum botching up a few frames and forcing you to cut it into 2-3 shorter timelapse clips
White Balance = K. Manually set your white balance, keep it out of auto, i have run into issues where the flicker in some lighting scenarios can cause the white balance to shift from time to time, causing a timelapse where the resulting footage flickers from one hue to another repeatedly.
ISO = Manual, Lowest native ISO you have. I do not mess with the extended ISO, they generally come with a cost of suffered image quality. The degradation may be virtually imperceivable, but there is generally no reason to shoot under the lowest native number, you can always add a ND filter instead.
Image Review = OFF. Depending on the camera, if this is set to on, with no time limit, it may stay on the screen until it gets a half-shutter press, which may be next time it takes an image, and it may or may not take that image. I had once time where i was shooting and the first shot would take a frame and result in an image review, the next shot would turn it off, the third shot would take a frame and turn on the image review again, resulting in half the number of frames. I normally keep this off.
HDR Shooting modes, = OFF. You should have full control of the lighting, if you have to use some sort of dynamic range extention trick you are doing it wrong, focus on your light levels and exposure. Sometimes when using any of the extended dynamic range settings it may not process one image to the next the same way , as a plant grows and takes up more of the frame and changes the information in the image, which could cause it to start processing slightly different at one point.
Image Quality = RAW. Generally I prefer shooting raw, and really enjoyed the simple easy of loading 1000 frames into Adobe ACR and making mass edit/crops on the fly. However, as many people know Fuji Raw files are difficult to work with, however their Jpegs straight out of the camera are fantastic, so i have been shooting exclusively Jpeg. Unless you are using the same cameras I am using, stick to RAW. Disk space is cheap these days, if you are worried about disk space go spend a few bucks and get a 2 or 3 tb hard disk.
Image Size = Largest size possible. This means that later down the road if you want to re process in 4k, you have the source files for it. there is no excuse for shooting anything under the largest size possible.
Long Exposure NR = OFF. You do not want this. Long Exposure NR will take a secondary frame after the first one with the shutter closed to establish a dark frame, that is used as reference to remove any unwanted noise. This is the same process used in astro-photography to stack images. It is not needed, and could introduce unwanted artifacts, Keep it off.
High ISO Noise Reduction = OFF. If you are using high ISO you are doing it wrong.
Basically shut off ALL automation, you want this to be setup 100% manual.
You also need to make sure you have a shutter release cable. I build my own, to do this buy cheap $3 shutter releases off amazon, cut off the controller, and solder the leads into a 3.5mm stereo jack. For the pinouts, I have been using this website for a long time now.