old database on clean install

I'm doing a clean install of 1.3.9b on my test site. I saved my existing database and files from recent upgrade of test site to 1.3.9b. (Live site remains 1.3.8a.)

Site began as 1.3.7 and assorted mods have come and gone, some with no uninstall files. My upgrade on test site went ok and almost everything is working, but I'm playing with a clean install to see if I can clear some of the cobwebs.

I see in myPhpAdmin that a clean database has about a dozen fewer files (or whatever you call them) than I have on my old database. I presume those to be leftovers from old mods with no uninstall (?).

Is there a way to tidy that up, short of doing a complete manual re-write of my catalog? And/or will they do any harm if left alone?

My intention is to install some, but not all of the mods I was using, and to add some different new ones. I wonder about having difficulty installing sql statements if there is old junk existing.

Copy/insert all tables that are ZenCart default from the Backup of the version that the DB is with the exception of the "configuration" table that contains remnants of the added/removed modules.
Keep the clean configuration table from the new inatall

Run zc_install and upgrade this DB

Install your 3rd party modules fresh to this new inatall/DB

Always backup before attempting any thing like this to maintain a fall back position