RSYNC recursive over Time Machine Backups identify unique files
Modifying Time Machine back-ups directly is difficult. Time Machine uses hard links and other tricks to work. So probably best to try and reconstruct the contents on a new drive.

I would divide the problem into parts:


Fix the folder names
Merge the folder contents


Renaming

You can automate the renaming of files and folders matching specific patterns. See Rename multiple files by replacing a particular pattern in the filenames using a shell script for a collection of approaches.

You could also use AppleScript or Automator for this task, if you need more involved logic.

Merging

rsync is probably a good starting point for extracting the contents from the Time Machine drive:


which is the rsync command to «smartly» merge two folders?
Synchronizing folders with rsync


If rsync does not quite provide enough for your needs, consider unison.

unison is designed to keep folders synchronised, with the merging taking care to ensure the destination contains only the latest files. Unison can be used on local folders.