Okay, I’ll try to give my input here, because I’m very interested as well.
The original cylon detector. It appears that it did indeed work. I can’t really remember what Gaius thought about it though. I do remember him quickly flipping it over to read negative. However, I kind of always felt that they didn’t really need a cylon detector once they knew there was a limited number that they knew and who they looked like.
Secondly, you’re going to get the argument that the final four are different anyway. That’s gotta be the deal. Hell, we know for a fact that Tigh had known Adama since the FIRST cylon war. Unless Adama is the final Cylon. So the 4 are different somehow. Plus I think it’s safe to say that there were no humanoid cylons in the first cylon war, correct? I realize that original BSG isn’t cannon, but i think we can infer it from the fact that they were surprised to find it out in the first place. And before that we have, “Man created machine.” So somewhere we have the final four living on earth before the invention of cylons. Unless you want to say that the cylons invented the humanoid versions, placed them on caprica, started the first war without them, then started the second war with their other versions.
It also seems pretty obvious that the 4 never had copies of themselves running around. Say what you will about the other three, but Anders was famous. That’d cause problems right there if there were more than one of him.
Does anyone know the answer to this question? Is it ever made clear as to the whereabouts of the final four? I think it’s pretty interesting, right. The cylons apparently don’t know where they are because they entertained the possibility that they are on Galactica. If they were tucked away on a basestar somewhere, you think someone would know it. So I guess it’s safe to assume that they aren’t on the cylon ships. Which makes me wonder… where else do the cylons think they could be? They just nuked the 12 colonies. There are other places that are known (Kobol and Earth) but after that, that’s it, right? Seems to me there is Earth, Kobol, the Colonies, and New Caprica. But they found New Caprica. So maybe that’s why the Cylons want to get to earth. Maybe they think the final five are locatd there.
Also, is it just me, are you guys getting cabin fever? I was checking some of the earlier episodes, and it was kind of nice to see some land-based action. We first had Helo and Boomer on Caprica, then Starbuck went back, then we had New Caprica. We also had that algae planet, etc. I’m guessing there won’t be any now until we get to Earth… 
I had a thorough reading of the BSG wiki the other day (Not the wikipedia one, but another one) and it’s very informative. I’d suggest reading about the 12 Colonies, because it essentially gives a good idea of what has happened in the mythology.
What is strange now though is there is a lot of heavy focus on the “one true god” Does that mean that all of the scriptures are worthless? I kind of doubt it since they have been right up to this point. This obviously involves the pop-tarts in some way because I remember them having such a huge focus on cylon-human hybrids earlier on.
Personally I don’t know what to say about this religious bent to it. Head Six has been talking about this religion stuff forever. Baltar went from openly laughing about it, to kind of believing it because he’s having such good luck, to actually believing in it.