Ouch. Yes, resizing would have helped a lot. But...um...you really wanted to do the resizing much earlier in the process because, as you've noticed, it will break things.
You have two choices: resize and recreate or deal with longer render times. If you're working in CC 2015, I'd recommend opening that project file and rendering in CC 2014 (as long as your computer has 16 GB of RAM or more) because CC 2014 has multiprocessing which might make things go faster.
your pre-production planning should include image size. You basically want your images to be at 100% scale or very close to that at some point in the composition. If your image is a 3-D layer then at some point in the composition you wanted to be no farther away from the camera than the zoom value.
I think you are kind of stuck unless you can pre-compose the layer without moving all attributes to the new composition then replace the footage in the pre-comp with the smaller version, then scale up that layer so it matches the original image size. I do not know if that would work, but it is the only thing I can think of that may maintain your animation.
Do you happen to have access to a faster computer? I ask that in all seriousness. That will help with render time (of course, be mindful of computer specific dependencies like fonts and 3rd party filters) with the least amount of work on your end.
Although, I'm guessing that if you had access to a faster computer that you wouldn't have posted your forum question.
Have you tried setting proxies? On your hard drive, make duplicates of each source footage file. Reduce each duplicate's Image Size to 25% in Photoshop. Set the duplicate file as the proxy for each corresponding source footage item in After Effects (File > Set Proxy > File...). As long as the proxy is proportional to the source footage, everything will align correctly. When you render, be sure that Proxy Use is set to "Use All Proxies" in the Render Settings.
It's a reverse use of a proxy file that's a low-resolution duplicate, but you should notice a speed improvement and since the originals are all scaled to about 21%, the rendered quality should be good (of course, that's the most important part to keep an eye on).
Thanks everybody. Warren I'll give the proxies a shot, haven't used them for something like this yet. All in all though, it definitely sounds like I needed to resize the images before starting the project in AE.