Welcome to the forum!
This might or might not have something to do with the problem. There's nothing inside the page border. The easiest way to fix it, is Ctrl a (select all), then File menu > Document Properties > Page tab > Resize page to contents. That will put the page border around everything in the file.
This could be what's causing your problem, or at least part of it, although I'm not sure. There is some Flowed Text in the file. Most of the text is converted paths already, but there is some flowed text. Flowed text is only recognized in Inkscape. No other programs can use it (or even "see" it).
To find all the flowed text, open Object menu > Objects (it will take several seconds to open, because the file is fairly large). Then scroll down through and find all the items that say "flowRoot....". If you click on them in the dialog, it selects that item on the canvas. Then you can do Text menu > Convert to Text. Watch the text as you do that, because sometimes the text might move. But you can just grab it and move it back, if necessary.
I notice that you're using version 0.91. If I'm not mistaken (and I could be) there was a problem with transparency causing trouble in PDF exports in that version. I see some of your swatches have some transparency. So you could try either making those not partially transparent, or upgrading to 0.92.4 (where I think it's been fixed).
To be honest, I don't know if using the Swatches, itself could be causing a problem..... Are you required to use them for this project?
I guess you could make all the other changes, and try the export again. If you correct the text, page border and transparency, and you still have trouble, that would probably point to the swatches.
If you end up upgrading to 0.92.4, and you still have the problem, we'll investigate whether there's a bug with swatches. I'll search the bug tracker after I post this, but I don't have time to test it at the moment. But let us know if you have problems after all the other things are fixed, and we can test as well.
