Zenphoto can certainly support large images, the problem is that your server can't
For a "research project" I'm sure you could either run the server locally on a decently powerful desktop, or get a good VPS or dedicated server plan that you can set the limits on manually. For those images I'd recommend at least 512MB of memory for the server, and over 150+ made available to PHP through the php.ini setting.
Unfortunately on your current server no image gallery software would be able to resize images of that size.
But, your other plan sounds good too since the theme is easy to customize - if you make the names the same and just change the extension or something, then I'm sure you can deduce the filename of the larger image.