Should I emulate the n64 version or should I play the x360 one?

absolutely. B-K is a better overall package but B-T is still amazing.

Personally I like Tooie more, a lot of it's criticisms like back tracking and lag are not without merit but it does a lot more good than bad. And it's no where near as an autism test as DK64

The real question is, should you emulate N64 with Mupen64 or emulate the 360 version with Xenia?

The game did a lot wrong but it also did alot of things really right. Grunty Industries and Jolly Roger's Lagoon are amazing in how linear they actually are while still having 10 jiggies. Hell the fact you need to find the Talon Torpedo just to get to the next area of Isle of Hags is a testament to the level design.