Please review what you've done against:
https://docs.moodle.org/30/en/Upgrading#Standard_install_package
Some of the mod directories missing should have been included in the zip/targz aquired from Moodle.org. They are 'standard' mods .. ie, comes with every version.
In the link above, it does say ... any additional mods/blocks/themes residing in oldcode directory should be copied to the same locations in newcode directory .... *before* starting the upgrade.
Do hope you started the entire process with a backup of your DB and backup of the code. Always ... *ALWAYS* ... the first step in upgrading to higher version.
There have been many changes in code from 2.3.x to the highest 3.0.3+ code - what you are doing is what I've called 'hyperjump' ... skipping 2.4, 2.5, 2.6, 2.7, 2.8, 2.9. -> 3.0.3. There might be some hickups awaiting you with such a leap.
If there was nothing in the 2.3 why upgrade? Why not install a fresh 3.highest?
'spirit of sharing', Ken