I'm going to come at this from the freeware angle (I know you asked specifically about Nuke or After Effects but u/effectsfreak pretty much summed my thoughts up exactly).
If you are looking to not throw money at knowledge rather than software, I would suggest Natron or Blender. Natron, because it is basically Nuke without the built in 3D system, and Blender because of its 3D capabilities (i.e. camera tracking, particle systems etc.). Blender also is great for the motion graphics stuff that most people look for in AE - with the added benefit of being a full 3D package.
One added bonus is that both Blender and Natron don't require the computer specs that AE and Nuke do. So you can most likely run them on your computer right now and test it out.
This is just one other perspective. Best of luck on your journey. Compositing is so much fun!
Radeon RX 6900 XT is not on the list of supported GPU's at this time. That doesn't 100% mean that's the problem. But it very well could be that Nuke isn't able to locate "a supported gpu."
There are probably ways to force this but that's beyond my expertise.
What exactly isn't working? You're actually lucky in this regard because .nk files are quite literally xml scripts themselves perfect for line-by-line version control like git!
Obviously however, anything sourced by nodes in the comp won't be tracked if they aren't in the same "repo" folder but that's just the nature of git. If you are looking for a way to have a single repo to track everything in the nuke comp then you could make use of git submodules(https://git-scm.com/book/en/v2/Git-Tools-Submodules) which would let you treat each asset as a separate "sub" repo to your nukescript. But tracking massive EXR sequences in git is probably not going to be pleasant..
Here is the link you are looking for : https://www.blackmagicdesign.com/products/davinciresolve/
Fusion is free up to HD I think. And if you really have to use Nuke, you should still download Resolve studio so you can convert all your files from MP4 to ProRes or an image sequence so you can "upload?" them.
If you want to convert the whole CR2 sequence to EXR, I’m pretty sure Darktable will help you with that: https://www.darktable.org/about/features/ It was used to get us EXRs on a stop motion film we were comping. I think the only downside is the EXRs were tiled as opposed to scanline. But they might have fixed that in the newer version.
In Nuke, the CPU acts much more than the GPU which only works on a handful of nodes. What you really want tho is to get yourself a suitable amount of RAM. Maybe have a look at this site as well: https://www.foundry.com/products/nuke/requirements officially, the GPUs from the iMac aren't supported, but could still work well enough. Personally I'd get the 16GB 5700 XT to utilize the power in other packages than Nuke as well. Regardless which CPU you use, I'd aim for a 128GB kit, 64GB doesn't really cut it anymore these days.
I 2nd u/PotatoRecipe regarding PluralSight and fxphd. PluralSight depends heavily on the course, some are real rubbish, but some are really really good. fxphd has a very high quality level of tutorials, sometimes you watch if for something general and suddenly there's an excourse and you learn something amazing just as a side-effect. But comes at a price.
I also 2nd his other words: Foundry has a pretty neat own learning channel: https://www.foundry.com/products/nuke/tutorials it's not always the way you'd like it, but usually short enough to keep you in.
And to 2nd a last thing, Steve Wright. But not only for the books, also his tutorials; sometimes they are a bit too long if you know what I mean, but great advice and technique. I think he works for Lynda these days, there's a show called Nuke Nuggets IIRC, which is also quite nice
The Foundry's own "Getting Started Guide" PDF is a pretty great resource for getting a solid grip on the foundations. Just read through it and mess around with your own images and videos until you understand how the nodes in each section work. From there you can move on to the more comprehensive "Nuke User Guide" PDF for more advanced topics. By the time you've worked through both of those you'll be in pretty good shape. I haven't found a more authoritative or complete resource for starting out than those (I worked through several 3rd party Nuke learning books but found them patchy at best compared to the Foundry's own guides, which already cover everything other books do and more)
Would also highly recommend first of all reading a book about how multi-channel compositing works at the technical level, which really helps put everything else you learn into context so you actually understand what's going on. In the end, it's all math. I found this book an invaluable resource in that respect.
There's also the VES Handbook of Visual Effects, a massive tome which contains detailed and highly useful information covering absolutely anything related to VFX practices and techniques from basic to highly advanced. It's expensive, but totally worth it.
Check out a browser plugin called "clip converter" to grab videos from Youtube to mess with, there's a ton of green screen videos on there you can experiment with until you're able to produce your own.