yup, for instance, I have tested a Gibson Les Paul Standard with burstbuckers and compared it to my friend's Epiphone Les Paul Standard which he modded by replacing the electronics and hardware with Gibson stuff up (ie. burstbuckers, gibson 500k pots etc) and I find that the Epi can sound close to the Gibson but it cannot be a Gibson.

As with the quality of wood, how do you determine this? You see, I was specualting that maybe higher quality woods are the ones that have a tighter grain while the lower quality woods are the ones that have a looser grain because its the tight grain wood they use on Gibsons while they use the loose grain wood on Epis. That's why I was thinking, maybe this is the reason why Epis and Gibsons sound different?