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Navigation is something most of current readers don't do well. The situation is somewhat better on those that have a touch screen, such as PRS-900. However, the limited refresh speed of E-Ink still matters a lot.
LRF, also known as BBeB, is the original native format of the Sony Reader. It's still supported on all models. It is quite simpler in structure than EPUB. However, I don't think that a 3200 pages book will work well in LRF either. What I would suggest is to look at the actual file you generated, not just run it through a converter and hope it works. Two things you should try:
1) Split the book into smaller XML fragments. If you have big chapters, try to split them by section, or for example by groups of hundred drugs or something.
2) Look at the HTML generated and see if it can be simplified. Remove any redundant HTML. Try to use a common CSS to adjust the look of the text instead of inline styling.
Check our EPUB forum, there is plenty of people who know EPUB quite well and might know extra tricks. Post fragments of your book and ask for advice.
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