Amazingly, I found a simple way to get a file out of the .xsn package!
There's actually a function in the object model to do it:
this.Template.OpenFileFromPackage(fileName)
There's a good example here:
http://theressomethingaboutsharepoint.blogspot.no/2013/01/infopath-managed-code-c-to-convert-view.html
When it comes to the problems I'm having with the rendering, I'll probably come full circle and try to make this.CurrentView.Export(@"Export.pdf", ExportFormat.Pdf) work.
It's unbelievable fickle though, with borders disappearing if the width or height is somehow off (or maybe it's the weather or cosmic radiation that's the culprit... :) ) If anyone have any guidelines on that, I'll be happy to read it...
Hilary, could you show me how you did that conditional thing with replacing checkboxes with Wingdings?