Sorry Adam, just noticed your reply.
Got it sorted (mostly), took it to a professional and it turns out that when I replaced the left side engine cover I didn’t tuck on of the wires to the sttor away properly and it got chewed out. Luckily it was the wire for the lights and stough and not the one to the ignition or I would have ended up stuck somewhere. All the lights are working again now.
I also thought the battery wasn’t charging properly but it turns out the starter motor is dying and needs to be replaced but I will worry about that next time I am home.