Hola Julie

The meaning of the sentence in the lesson is:

Si vinierais, os haríamos una paella riquísima.

If you came (if you were to come) we would make you a tasty paella.

So, in the event that you came (if you do, hypothetical) we would do it. 

I think, in your other sentence "if you guys came, we would have made ...." you´re mixing a bit the combination of tenses. To say "if you guys had come, we would have made you a paella" - for this situation that is seen as not possible as it's saying "if you had come...(but you did not come).." you need in Spanish:

Si hubiérais venido, os habríamos hecho una paella. 

The last example you write: "if you guys come we would make....." you're also mixing tenses a bit. I think what you need is "if you guys come we will make you a paella.", which is the natural combination of tenses in this case. For this you need in Spanish:

Si venís, os haremos una paella. 

I hope this clarified it. 

Saludos