That's probably a good order; you may also wish to remove all "target" attributed in A tags, which I believe you can also do with HTML::Parser. This should deal with the problem of navigation issues. Also, you'll have to play with COLSPAN and ROWSPAN attributes of the table cells if you have anything more complex than 2 frames.
Alternatively, if you have your own server with SSI enabled, you can include the text of other HTML files (head/body tags included) directly, so you'd only have to write out a table body with the various include tags, and that will get the job done too, though the final document will not necessarily be HTML4 friendly.
Dr. Michael K. Neylon - email@example.com
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Posts may use any of the Perl Monks Approved HTML tags. Currently these include the following:
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