The rotated pasted text is the consequence of differently oriented pages in their original documents. That depends on how the document has been created, and can not overcome except by recreating the PDF with controlled settings.
The workaround would be using a tool for "last second editing" in the prepress industry, such as PitStop. If I remember correctly, you can rotate text in PitStop, so that would solve the problem.
Another workaround would be using Illustrator as a helper. However, you may lose other features of your document in this case; you'd have to check whether tags and structure are still intact, for example).
Hope this can help.
Max Wyss.