This is an intricate sentence, but as you are advised in the comments, you can simplify it by taking inessential clauses out, so as to make out the basic framework of the sentence.
In other words consciousness is an illimitable power,(1) and yet there is something (2) that holds one in one’s place (3), makes it a
standpoint in the universe(4) which it is probably good not to forsake
This is the basic structure and I think it is not difficult to grasp. In the independent clause (2) (and there is something), there is one subordinate of concession:
and though at times it may seem to be all consciousness of misery, yet [other missing clauses] there is something
(so although it shows you misery, there is something positive about consciousness)
The missing clauses left show the way in which consciousness brings its positive support to our being.
[How does it do it?] in the way it propagates itself from wave to wave, [in what purpose?]so that we
never cease to feel, [do we really never cease to feel?]though at moments we appear to, try to, pray to
In though at moments appear to, try to, pray to the subject "we" is omitted twice and the embedded clause "cease to feel" is omitted three times. So you can read it as:
though at moments we appear to [cease to feel], [we] try to [cease to feel], [we] pray to [cease to feel]
EDIT: In clause (4) it refers to "consciousness", so you can re-write it as:
(there is something that) makes [consciousness] a standpoint in the universe.
In clause (5), "a standpoint in the universe" is replaced by the relative pronoun which. It here is a dummy it:
which [a standpoint in the universe] it is probably good not to forsake
it is probably good not to forsake this standpoint in the universe
Which [a standpoint in the universe] is the direct object of the verb to forsake, so where would make no sense instead of "which".
I forsake the world - the world which I forsake