Problem with Buttons/Form Fields in Acrobat PDF when created in InDesign CS4

So I have been working for quite some time on an interactive form for an internal client at my job. It has two major components, one is the side bar navigation, which I created using buttons in InDesign which link to bookmarks in the document. The second aspect is that I also created "check boxes" accoring to this video: http://www.adobe.com/designcenter/cs4/articles/lrvid4434_ds.html
I have two major issues:
1. Whenever I try to convert my boxes to form fields in Acrobat it will not recognize them unless I save out 4 pages at a time (rather than the whole document).
2. I then have to combine the document and get multiple sets of bookmarks, and some bookamrks are corrupted (not working properly). Even when I try to convert the whole document some of the buttons are corrupted.
UGH tired of this project, I am really bastardizing the whole thing to get it done, but want to figure out the problem as this is an ongoing document that we will be using over and over again in future years.
I am attaching the pdf file--this is a pieced together one (saved out 4 pages at a time) (which I did do some fixes to to get buttons to go to proper locations) and the original indesign file (partial file due to size).
PLEASE OH PLEASE HELP ME!

Acrobat's Form Wizard is good but not perfect when creating form data from a PDF. I have never encountered Acrobat not able to finish the process of creating all form fields, but have encountered very slugish performance afterwards when there was a lot of forms, buttons, and other elements within the pages. And I would say, from your attached PDF, it is pretty heavy with content. I am going to suggest an idea, but I have not tested this to see if it would work.
In InDesign, create a layer for your navigation tabs, and a layer for your text with the check boxes. Create two PDFs from ID, one PDF with just your-nav tabs, the second with just your text with check boxes. In Acrobat, perform the Form Wizard on the second PDF and see if this will finish, the idea here is to reduce the cllutter for the Form Wizard to finish. If it does, you can merge the first PDF as a layer with the second to have a completed document. Again, I have not tested this theory.

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