here is a list of plug ins used

ceon url mapping
google merchant senter feeder (need to uninstall)
products with attributes stock
Ceon Sage Pay Form v2.0.3
Product Listing - Layout Style column plugin (product_listing.php)
database backup mysql
export email addresses
gift wrap

out of these it is only gift wrap that has code in similar files, but i have been very careful to merge properly keeping all code intact

i'm not sure excatly what you mean by the source of the zc store files, but i recently upgraded zen cart to 1.5.3, the files from standard zen cart download

im not sure what you mean by how i upgraded, i just upgraded like you normally do,except it ook me several tries and to this point a few days trying to make sure all files are merged/uploaded correctly