There is much history on your upgrade:
http://www.zen-cart.com/forum/showthread.php?t=32737
http://www.zen-cart.com/forum/showthread.php?t=37201

It seems you have had troubles with code not working while installing upgraded PHP files for v1.3.0.1
It seems you've had troubles copying selective data from old database to new.


This is a harsh statement, but must be said: it seems you think the upgrade instructions are a waste of time ... but yet when you follow another approach, you want us to fix your mistakes.



Now ... if you wish to continue along your own line of upgrading in this manner, why not install a fresh v1.3.0.1 site, and selectively move your data to IT ?

In fact, try a fresh install of v1.3.0.1 with demo data, and check to see whether deletes work or not. If they do, then clearly your cases of deletes not working are related to files on your server not being up to date..... which it would seem to me is the problem.