I downloaded an e-book from iBooks earlier today i ... some of the text and diagrams are a bit all over the place.
Is the anything I can do fixed them?
I've tried to convert to pdf and then to word but that just makes things much worse.
...
Converting to another format will never automagically fix problems with the original file.
The best method and tools to use will vary somewhat with exactly what format the original format. I second Patron22's recommendation of calibre, primarily for its editor more than for its conversion ability. I also suggest that you get
Sigil, a pure editor. Both calibre and Sigil are free, so get both.
I also HIGHLY RECOMMEND joining the
MobleRead forum. It is an excellent resource for all things "ebook", including being the primary calibre and Sigil support forum used by the development teams for both apps.
The primary iBook format is a bastardized variant of ePub. Depending on the source and download method, you may find that you need additional tools to reassemble it into a more conventional ePub so that calibre's editor and Sigil can deal with it.
Also, iBook's fixed layout variant is quite different from the ePub3 fixed layout variant and both are different from the Amazon Kindle/Fire fixed layout format. Converting between any two of these requires a massive amount of manual effort.
Given the issues you have, it may be that you have a standard ePub3 fixed layout ebook that iBooks is failing to display properly. You may just need a different ereading app that handles standard ePub3 betters. It may also be that the ebook was generated from a PDF that was itself generated from the page layout file used for a print version. If the latter is the case, you'll be in for a lot of manual work to "fix" the file.