So I think I can get this to work. The docs, especially the ones at http://www.zen-cart.com/docs/ look like great reference.

Needed to update the database to 1.3.9 from 1.3.8 which was easy, just exported from the live store and imported it into my localhost database (yeah, there are actually three databases involved but the local and the new host are in sync.) where I ran the install/sql/ patch to bring it up to date.

Then it I exported it again (all import and export through phpMyAdmin) and ran it against the export from the new host database in FileMerge. Here is my strategy...

The tables to change are:
address_book; authorizenet; coupon_redeem_track; customers; customers_basket; customers_basket_attributes; customers_info; orders; orders_products; orders_products_attributes; orders_status_history; orders_total; products; products_description

not sure about:
counter; counter_history;

the rest of the changes are in the configuration of the site, things like ez-pages, which I do not want to change.

thankfully I have not made any changes to the catalog of products, and the only differences are in inventory and view count. I could probably leave those alone.

So when the merge is done (merging the changes and additions from the live site in) the dump file should look like it came from the live store, only configured visually to match the new store.

Only other concern is the new store has database caching enabled. Hopefully that wont be a problem. Or maybe I should turn it off before I import the new dump?