Okay, that clears things up a bit.
For the site that isn't showing all the features, try uploading the mojoPortal files again. I think some stuff didn't make it. If you are using FTP to upload the files, try using FileZilla. I find that it is the most reliable and it shows you a list of files that didn't make it and allows you to easily try uploading them again. You may also want to upload the files in this order:
- Setup folder
- ClientScript folder
- Data folder
- the rest of the files
If you have made adjustments to the web.config file, make a note of these before uploading the new web.config. You must use the new web.config when upgrading because there are usually updates to it and things will not function properly without those updates. For the most part, your changes to the web.config file will be in the <appsettings> section and all of those can be placed in the user.config file. This will make future upgrades a lot easier.
Once you have the files uploaded, go to http://YOURSITE.COM/Setup/Default.aspx. This will run all the necessary scripts for installing and configuring all of the features.