Have you been in contact with Legacy Support to try and solve your problems?
Have you submitted a bug report for things that are not working properly, or suggestions to improve those features that are working as they're intended but could be better?
There are programs that will edit a PDF file for you - I can't name any right at this moment, but I'm sure you'll find something with a Google search if you want to persue that.
What word processor are you using? Have you looked in its Help to see if it can index for you?
Are there any specific questions we can try to answer for you?