How can a non-dense, well-ordered set like a long ray be uncountable? If it's a set of an uncountable number of [0,1) line segments laid end to end, shouldn't there be a bijective function between the COUNTABLE set of natural numbers and the n-th segment on the ray? Is its very existence not a contradiction?
The idea behind the long line is to take $\omega_1$ copies of $[0,1)$. If the [non-negative] real numbers can be thought of as a countable union of $[0,1)$ ordered lexicographically, the idea behind the long line is that we take even more.
The fact that there are uncountable sets which are well-ordered follows from the axioms of ZF, it does not even require the axiom of choice.
The long line, if so, is not like a subset of the real numbers. It is a whole other topological space. In that space there is an uncountable well-ordered set, whereas in the real numbers every set which is well-ordered [in the natural order of the real numbers] is countable.