Complicated site transfer

I’m transferring a site and having some issues.

The original site was at domain.com/wordpress because they currently have a site on the root. Last minute they decided to change hosts, so while I’m at it, i figured i would put it on the root of the new server.

They provided a host (godaddy) which had wordpress pre-installed. the DB had a different prefix from the previous host. So I downloaded the SQL, edited the prefix within, cleared data on the new DB and uploaded. I switched the site URL and I can see the site (almost perfect).

I went to login, and get insufficient permission error. I looked up and found a force upgrade script — which worked (sorta). I can now login to wordpress, but the menu is gone. I can’t access pages, plugins, appearance, etc. Before I transferred the site and just logged into the default WordPress site, the menus were there, so some link must be missing between my new DB and the WP interface menus. should i check my wp_content folder? is there something in my DB that links it all together? could use some ideas.

Thanks!