Assuming they're not DRM'd (or you able to and have no ethical problems with removing DRM), use Calibre's conversion tool on them. There is an option to split large files into, by default, 260k chunks. That should keep your Touches from puking when trying to navigate. The formatting will likely suffer a bit, though.
(dunno about the issue of it not loading the large files, though - mine had no trouble when I loaded a couple of 60MB comics (.cbz) archives onto it to see how bad it'd be; the results were horrible and I'd really love to see a fit-to-width landscape mode for .cbr/.cbz)
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