First of all, there are different armor pieces and such that you can download, but I don't know how to apply them. Secondly, after playing with the models a bit, I noticed there is an armature in almost all of the models called "weapon_R/L". Is there a way to apply the weapons to the armature? Thanks in advance
From what I remember you need the basic Link body and the armor you want. Remove parts from the Link body that the armor will cover.
The hard part is the armatures. If you have the Link body and Champion's Tunic. You will need to merge each armature to to make a common armature. This means removing common bones that both armatures have and while doing this make note of bones that are linked to a bone that you are about to delete as you will need to re-link the bones back once the armatures are merged.
I think all you have to do is snap the weapon to the weapon_R/L bone and it will be in place. Scaling may need to be done. To make the weapon move with the rest of the body it will need to be assigned to the body armature and the weapon it self needs to have weights assigned to the weapon_R or L bone.
The above is for Blender 2.78c.