Seriously that's a lot of hassle for people to manage trying to find the site let alone a shop. I would tell him he needs to get a separate server setup for the thing and definitely a domain name that points directly to the shop site at the very least.
Other than that, I would also suggest that you upload the shop into a /shop directory rather than the main domain unless that's all that is there. Chances are if he had things there and had anything named the same, they got overwritten with the shop files such as a index.php file or something like that.
If nothing was there to start with then you're all set, but if he plans any other pages to go there that will be done outside of the shop pages, I would suggest a /shop directory so that they are separated. This way an uninstall of the store won't lose externally created pages as well.
Basically you would end up (at this time) with something like the same address you put into the cart for the address the first time with /shop on the end.
Hope that makes sense, kudos to you for trying to work with that mess lol. Good luck
