Update 2:
I managed to get loot working again, this time without the need to edit any of the loottable or lootdrop tables.
It seems the tools to create the PEQ tables found here:
https://www.youtube.com/watch?v=wn711Rt4I20 are missing some connections.
When I used the latest PEQ db found here:
https://db.eqemu.dev/ it worked without needing to edit the loottable/lootdrop tables.
Just putting this here in case anyone else faces a similar issue but this has been resolved for now.