For the long term the use of an authoring application having effective Tag management associated with the PDF output process would make a difference (e.g., FrameMaker, InDesign, MS Word 2010 using the MS process or Acrobat's PDFMaker for MS Word).
As to the PDF in hand. Did you start by using TORU's marquee to set each table cell to "Cell" and after all are done using the marquee to bound it all and setting it to "Table"?
Note that this would be a page at a time. After that you'd establish table header rows then header cell(s) span / scope as appropriate. Remember the table description.
Even for a smallish table this is a time consuming process and "oops" can be frequent.
Save As frequently.
Since we use a contractor for our graphic design and typesetting, were kind of stuck with the PDFs we get.
At the advice of US DHHS's web site on 508, I had been trying to do the opposite of what you suggest--namely, create the table first, then create the cells. Trying it the opposite way, I got one big cell--meaning, when I selected and tagged a cell, Acobat automatically made it part of the cell created before it. But checking the content list showed that each table cell was contained in its own < TD > tag...so far, so good. Then I tried to contain megacell in a table tag and Acrobat crashed again.
Thanks for the detailed reply and getting me one step closer.
Two sides of the same coin (cells first - table first). Either way manually tagging tables (or any tagging via TORU) is a chore that often just does not get the job done.
In retrospect I ought to have mentioned my typical default approach to manually tagging a PDF.
Scope the document contents. Outline what tags are needed/appropriate.
Work out of the Tags panel. Add tag(s) to the Tags panel, leave focus on the desired tag, with the Select tool select specific content, back to the Tags panel's Options menu to create tag (which puts the content under the tag of focus.
For a table this'd start cell by cell.
Bottom line a primary success precursor, when manually tagging, is to not use TORU.