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In my experience PDF files that are that large tend to have complex layout that does not convert well. Alternatively they have a lot of graphics and they will be large regardless of the format.
With an iPad I suspect that you will be best off keeping them in PDF format. The form factor is large enough that you can normally get away without converting to a reflowable format such as ePub. You may find it worth investing in an iPad app such as Goodreader that specialises in PDF handling.
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