Rendering a production master as an MP4 using the YouTube preset is most obvious beginner error that I see. NEVER use highly compressed video as a production master or DI (Digital intermediate). You can't see them but there are statistically huge compression artifacts in any MP4 rendered for delivery to the public. When you try and render the footage again and re-compress the footage, these errors grow exponentially and seriously degrade the image.
The other problem with using MP4 files in your project as a DI is that there are more frames of video that are made up of calculations the CPU makes by looking ahead and behind the current frames in the film than there are actual frames with individual pixels. That's how compression works and when PPro or AE starts decoding the original MPEG MP4, if there is any hick cough caused by cache or pipeline or effect issues the creation of these artificially generated frames can get fouled up.
You should use a visually lossless format for your intermediate renders. Pick a good one and stick with it. JPEG 2000 or PNG codec Quicktime are both fairly high quality visually lossless frame based and alpha channel supported formats that are suitable for use as a DI. I prefer the Cineform codec available from GoPro because it is 10 bit (that's millions of more colors), visually lossless, and supports alpha channels. If you want the highest quality render your DI as a 32bit tiff sequence.
The other problem may be that your system is just not up to the requirements for 4K production or that you don't have the frame rates down. If you are going to do 4K do not use 60fps (don't know what the frame rate of your project is) because it is not necessary and any hope for a cinematic look to the product is going to take a lot more work and may not work at all.
I also probably wouldn't export as jpeg's from lightroom. I'd pick a more visually lossless format, and I would resize the export to the final size of my video. If you plan to push in on your time lapse and fill the frame with only a portion of the frame the image sequence larger than the frame size of the final video so you never scale above 100%.
If you export the image sequence from Lightroom at the right frame size there is no reason at all to re-compress the footage to a movie. PPro and AE both support image sequences as movies, they render very quickly, way faster than MPEG movies, and you can set the frame rate to anything you like. About half of all my DI's are 32 bit tiff sequences because they are headed off to another artist or editor for further work before they are made into a movie.
I hope this helps. You should spend some time studying up on production techniques for time lapse. Most of the YouTube tutorials on the subject are from amateurs that don't really know what they are doing. Make sure you vet your trainers. I've been doing time lapse for film and television since 1972 and I know what I'm talking about.
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