For future reference, you shouldn’t go “deep” at all – you should be copying everything, even if a particular folder is empty. You should also invest in a program such as ShotPut P2 or ShotPut Pro, which will copy your files for you (and in up to 3 locations simultaneously) and perform a verification check.
You still need a “Contents” folder that the other 6 folders will reside in.
As for the LASTCLIP.txt file, that would normally be next to the Contents folder.
Check out “Shane’s Stock Answer #38,” by Shane Ross, for the way to recreate your LASTCLIP.txt file:
https://library.creativecow.net/articles/ross_shane/fcp_faq3.php
-Scott