My first suggestion would have been to try easypopulate, but sounds like you're having trouble getting that working. (we routinely do imports for 6000+ items, so I feel your pain, but thankfully we've had pretty good success with EP).
An alternative (not the most elegant) could be a mysql update to remove the unwanted junk. On a test copy of the database, run something like:
Code:
update products_description set products_description = REPLACE(products_description,'<html>','')
It works for me on a few quick tests.. although you'd need to run one query for each tag you want to remove (and then the closing tag) as unfortunately I don't think REPLACE accepts a % (wildcard) character.. This of course assumes you know all the tags you want to remove, and there aren't a ton of different ones. If you really wanted to you could write something to loop through and find all the values in <>, then loop back through and run the update for each of them - but this would probably be overkill unless you have a ton of unknown tags..
Might be an option for you.. if it works on the test database, save the queries you performed to a notepad, then copy/paste them into phpmyadmin and run on your live db. Of course, if you plan on doing much bulk editing in the future - I would strongly suggest troubleshooting EP and/or trying to find out what your phpmyadmin imports are choking on. I've run into timeout/filesize errors importing entire db's, but usually not just when importing table.