Thanks for all the tips and input everyone, they were super helpful! I wound up using a few different glues together for some great results.
I used a Gel Superglue (I used both a Gorilla and LePage variant) for PLA to PLA or PLA to rough resin, the gel consistency really filled the layer lines or rough areas well and bonded great!
For tiny parts, my local Home Hardware had Akfix 705! The two part system makes that stuff bond so fast. It was great to tricky to set parts, or for parts on weird angles.
I tried out Permabond 200, my work had some laying around. It bonds realllly well, but it was a bit too viscous for what I was doing this time.
I also tried out some clear UV printing resin, its just trickier to work with. However it gave everything a cool glossy finish. I used it as a finish coating rather than as a bonding agent in the end.
I’ve been trying to hunt down 3D Gloop, to no success. I just really want to try it now that I can’ t get it… 
Here are two quick pics of what I was gluing together now that the LED’s are in the base and the glues are all cured! It’s a bit of an odd one, but it was a custom gift with an inside joke.
The base that is hidden in the shadows is PLA with just a flat surface, I’m surprised things bonded this well!