New kindle. Help

You're making sense... big question is, did you send the book across as a PDF or did Calibre convert it to a MOBI/AZW file?

Either will work, but you'll get different results. Sometimes the PDF is better, sometimes the converted version.

Let me explain...

A PDF is fixed to individual pages, it's effectively an electronic "image" of a book - the pages are just the same as they are in the real book.

Now, if the real book has small pages (paperback books size), it will display on the 6" Kindle screen OK - each page in the book will be one screen in size.
However, if the real book is bigger - Letter or A4 in size, when you display it on a 6" screen, the pages will still be one screen in size, and as a result it's way too small to read.

An ebook, on the other hand (mobi or AZW) is the text of the book. It's not a fixed page size, so will scale to any screen (there will be more or less words on the screen depending upon the font you choose and the screen size). Navigation is by means of being able to jump through the chapters or sections of the book (which therefore depends on this information being encoded in the file).

Now, if you've taken a PDF and converted it to a mobi, you will probably have the variable size text, but you will still have all the "junk" that's at the top and bottom of each page - headers and footers, the page numbers and title etc - and you won't have any of the chapter information.

So, often with a PDF, your choices are either to transfer it as a PDF in which case you'll get a well formatted page which is too small to read, or convert it in which case you'll get words which are easy to read, but with headers/footers etc in the text, and no easy navigation.

I'm afraid all you can do is try both the PDF and the conversion, and see which you prefer for the particular book. There is no hard and fast rule, and sometimes both are pretty poor. PDF was never designed for e-book readers!

[I probably should explain that if you are prepared to put some work into it, you can do a good conversion. Calibre has a number of tools to remove headers and footers and detect chapters, but you need to tell it what to look for. Another approach is to convert PDF to RTF, open the RTF in Word, edit out the headers and footers, pick out the chapters or sections as headings, then convert the RTF to mobi/azw. A lot of work for a one-off book!]

Morf is spot on as usual.

I'll add that, if there are pictures and diagrams, those will come through in a converted PDF, but they won't necessarily be in the 'right' place relative to the text. Any layout -- pull outs, margin comments, graphics captions, etc. -- will be lost there, but possibly not in the place you expect them.

That said, if you mostly need the information -- a conversion may be all you need. If you can, as well, get the table of contents to stay linked -- won't happen with an automatic conversion, most likely, but you may be able to play with the software -- you'll probably have all you need. But, even if not, you can still search since the converted file will be indexed just like any other kindle book. I do not think PDFs are indexed, though, so they're not particularly searchable if left in that format.

I don't know anything, really, about Calibre -- sounds like you did a pretty much automatic conversion.

I think the software is powerful enough to make the ToC linkable. But I've got no idea how that works.

What you could do, as a work around, is take the time to find the chapters and put a book mark on each one. Then you can use the 'notes and marks' to navigate fairly quickly to the various chapters.

If you've sent the document via Amazon and it's archived there as a personal document, the notes and marks will even be synced across more than one device if necessary. The easiest way, I think, to do that is use the Send to Kindle applet: Send to Kindle for PC is available to download at www.amazon.com/sendtokindle/pc and Send to Kindle for Mac is available for download at www.amazon.com/sendtokindle/mac. (If you use this, you'd NOT want Calibre to send it, just convert it and leave the converted file on your computer.)