Can I possibly get Premiere to work for this project?

Question

Hi. I am working on a time lapse scanner photography project. I scan flowers a few times an hour and then make videos of them drying out. I'm currently making a movie of it all. The thing is, the scans can be thousands of pixels high/wide. The problem arises when I make sequences with 20 or more of these videos (scaled down to around 10% in Premiere) moving together. It becomes almost unusable on my older Macbook Pro. Doing the more complex parts of it is also very inconvenient on a new iMac. Because I'm working with so many files, I tried out After Effects. Its proxying feature excited me, but it soon became clear that AE is meant mostly for shorter projects, and not for clips that can get 40 GB + in size. For example, in trying to make tiny proxies of clips last night, only four succeeded. It seems that the rendering is centered on your available RAM, and when it runs out (a few seconds into the first clip) rendering becomes very slow. This might work for ads or something, but not for this project. Maybe I'm not using it correctly though.
So I don't know what to do. I've tried a proxy workaround for Premiere, but that seems to involve working with clips at the resolution you made the proxy at, unlike AE where you can work with a now-more-blurry version of your main file. I tried making a tiny proxy manually, and then upscaling it in Quicktime Pro 7, but that seems to also be slow for Premiere, leading me to think that multiplying the one clip in my test sequence by 20 or more wouldn't be that different.
Does anyone have any ideas as to how do edit a project like this with a reasonably responsive UI? I don't care if I have to spend hours rendering proxies, or rendering the final copy afterwards, I just want to be able to edit without waiting for minutes when I click on a 20 layer part of the movie. I understand that this is probably an abnormal way of using Premiere, as normally one only uses a few layers at a time.
Another idea I had was to do the parts of the movie with 20+ layers in AE, and import them in Premiere to get around AE's focus on shorter lengths. But this doesn't get around the issue that its proxying feature, and rendering engine in general seems to be tailoured towards shorter projects. If you are confused, that's okay, I can elaborate more and provide pictures.
Here's some single videos from the project:
http://www.momentaryvitality.ca/
Thanks!

Answer 1

ATI cards will not work for GPU acceleration of the Mercury Playback Engine and only Nvidia cards with at least 1 GB or RAM and at least 96 CUDA cores will allow for a good experience when using the GPU enable Mercury Playback Engine.  I have a mediocre GT 240 with 1GB of RAM and it rocks. It is much better than using the software only mode. Software only mode is not bad but GPU enabled is so much better. You will have to trust me on that. A new Macbook Pro would not be wise. In fact $900.00 Dell or HP with at least 96 CUDA cores and 1 GB of RAM would be a much better option. You could in theory get a mediocre $600.00 Quad Core from Best Buy and then buy either a $70.00 Nvidia GT 240 graphics card or even a $135.00 GTX 550 graphics card to put in the system. That would work just as well.