Ubuntu, I think I see the problem you're encountering in this whole methodology business. You're saying that there are no axioms in the methodology of science (that is, there is nothing that scientists must take on faith before proceeding). Well, getting around the fact that you're wrong, I can now see that you're essentially just trying to re-word the story in a way that makes it seem like you're right. Before I counter what you're arguing, I'll reiterate that in order to play a game of football, you must first take it on faith that the football actually exists. You don't go play football thinking "Well, if this football actually does exist, then I think it would be travelling along this trajectory to point B where I'm supposed to catch it in 4.35 seconds... if it existed." Instead, you temporarily accept the existence of the football (even if you do not know that it exists in fundamental reality) so you can play the game of football. Same goes for science. When you're going to play the game of science and try to measure matter/energy in the universe, you must (at least temporarily) accept the existence of that which you are measuring. Otherwise you wouldn't be measuring anything at all.
What you're trying to say is that scientists need not always accept the necessary existence of matter/energy (and its measurability) in order to play the game of science. Well, yeah. In order for me to operate within the methodology of Christianity, I must accept the existence of God and the Bible as the word of God--even if ten minutes later I want to stop playing that game. For the time, if I do not accept the existence of God, then I'm not playing the game of Christianity at all. Same goes for science. If I want to play the game of science, I'd first have to accept on faith the fact that stuff actually exists for me to conduct scientific studies with. If I don't, I'm not playing the game of science at all. But if I do accept that axiom from the beginning, and proceed to play by the rules of the methodology and come to conclusions within the methodology of science, then I have played the game of science. However, ten minutes later I can stop playing that game and no longer accept the existence of the stuff I just did.
What you're saying does not change the fact that science has axioms. Whether you accept these axioms as true all the time doesn't matter. That's like defining the Christian methodology as "Well, if God did exist, and if the Bible was the word of God, then..." However, that's only the beginning step of the methodology. In order to become a Christian for a little while, you must fully accept that which is being put forth as an axiom and then proceed.