Tough question! It seems that you're mixing up quite a few different issues here.
First of all, the 'which' modifier needs to be placed as close as possible to the noun that it's modifying. That's problematic in answer D, as we need the 'which' to refer to limitations, not money or any other noun. By repeating 'limitations', answer C avoids this problem.
Second, the use of a preposition before 'which'. This is also fine, it just sounds a little old fashioned. In speech I might say 'I bought a car, which I paid a high price for.' However, in GMAT, you're more likely to see constructions such as 'I bought a car, for which I paid a high price.' The word 'which' is still referring to 'car'.
Finally, in your (well chosen) examples, the problem comes with the word 'some'
(Right)The Achaemenid empire of Persia reached the Indus Valley in the fifth century B.C., bringing with it the Aramaic script, from which derive both the northern and southern Indian alphabets.
This is fine: the alphabets derive from the Aramaic script.
Right)Right: This model explains all known subatomic particles, some of which were only recently discovered.
Good. It was only
some of the subatomic particles which were recently discovered.
(Wrong): This model explains all known subatomic particles, of which some were only recently discovered.
Problem! What's the 'some' referring to? It's not clear that it's some of the particles.
I hope this helps.