There is a wide variety of errors in your post, but for the time being, I'm going to focus on what I consider to be your major error. You confuse the work of individual scientists with the work of scientists as a whole.
You mention two specific examples of assumptions that Darwin made: small changes can accumulate from generation to generation and, with enough time, produce "major changes" such as new organs or new proteins; and the earth is old. (I think you are wrong even that Darwin assumed these things, but I'll leave that for another time because it's not important to my point.) Even if you are correct that Darwin made these assumptions, that doesn't mean that all scientists made them, or that they are assumptions that scientists now make to support the ToE.
I would accept without argument the proposition that individual scientists adopt certain assumptions in the course of developing particular hypotheses. However, before any such hypothesis is accepted by the scientific community, those assumptions are tested to see if there is evidence to support them. If evidence conflicting with the assumption is found, the hypothesis is rejected. If neither confirming nor conflicting evidence is found, the hypothesis may still be accepted tentatively, pending the confirmation or refutation of the assumption.
A real world example of this process in action can be seen in the history of Wegener's theory of continental drift. Wegener saw various indicia that suggested to him that the continents were at one time all part of one land mass, and eventually separated. An assumption behind this theory would be that the continents were capable of moving across the surface of the planet. However, that assumption conflicted with that what known about the make up of the continents and the crust of the Earth. The continents are lighter than the crust, and ultimately Wegener was unable to provide an explanation for how the lighter continents could move through the heavier crust. Thus, his theory was rejected. Later, when it was discovered that the continents actually rode on plates that moved, Wegener's theory was vindicated and accepted by the scientific community.
I can in fact name an assumption that Darwin did make. He assumed that there was some mechanism by which characteristics could be passed from one generation to another. The scientific community was unaware of any such mechanism, but the strength of evidence behind Darwin's theory was enough for the scientific community to provisionally accept it. As you know, eventually the mechanism of inheritance was found, and the assumption was confirmed. But, at no point in time did the scientific community simply accept the accuracy of the assumption. Instead, it was investigated. And that is the key thing you should learn from this discussion.
Science, as a whole, never accepts any assumption necessary to support any theory. Scientists investigate to determine if there is evidence to support the assumption.
Ridicule is the only weapon which can be used against unintelligible propositions. Ideas must be distinct before reason can act upon them; and no man ever had a distinct idea of the trinity. It is the mere Abracadabra of the mountebanks calling themselves the priests of Jesus. -- Thomas Jefferson
For we know that our patchwork heritage is a strength, not a weakness. We are a nation of Christians and Muslims, Jews and Hindus -- and non-believers. -- Barack Obama
We see monsters where science shows us windmills. -- Phat
™ Version 4.2