I just read your post again that you dont want to upgrade because of all the changes you have made to the ascx pages. When you search for the product are you searching from the product listing page or the manage orders page? You could probably just add the delete flag in the where clause of one of the stored procs to fix this but I need to know what page your searching from.
Also, the cart uses your portal skins and containers so it shouldnt require any re skinning to make it look like your portal. What type of modifications are you making to the ascx pages. If you make your changes in the module.css then you could just restore your module.css after upgrading and not lose any of your changes.
-Scott