First you should understand the meaning of the sentence. It is saying that 'normally' (there could be other ways too) a bone becomes fossilized through the action of ground water. There are three ways, which happen in sequence one after another, in which the ground water fossilizes a bone.
A.
(Correct) Here the noun modifier 'which' shows the three ways in which ground water fossilizes a bone. Some of you might not realize what 'them' replaces. The only plural noun is 'organic components'. Hence this is correct and unambiguous.
B. Like in option A, it shows three ways in which ground water fossilizes a bone. However, those three elements are not parallel. The first two elements 'permeates', 'washes' are verbs whereas 'those are replaced' is a clause. When a modifier begins with
to be [verb], it modifies the entire preceding clause, similar to a comma –ing modifier.
C. three elements are not parallel like in A and B even though these are still the three ways in which ground water fossilizes a bone. 'to be replaced' denotes that replacing with minerals is the purpose of a bone becoming fossilized, which is wrong.
D. comma-ing such as 'premeating' and 'washing' should modify the main clause. However, the verb of the main clause is 'becomes'. comma-ing either provide the consequence of the main verb of the main clause or provides 'HOW' aspect of that verb. It is neither here. These elements describe how the ground water fossilizes a bone, not how normally a bone becomes fossilizes.
E. Like in D, these three elements should describe how 'ground water' fossilizes a bone, not how in general a bone becomes fossilizes. It lists three elements but the third element is not even separated by an Oxford comma.