There is really no need to go beyond 256 bit security. If you want to combine multiple keys - presumably because you are not sure they provide enough security regardless of the size - then you could concat them and use them as Input Keying Material to a KBKDF that provides extraction as well as expansion (e.g. HKDF). Then the output can be used to seed your PRNG.
It seems you are trying to build your own KDF using CTR mode. Such KDF's already exist, but they generally don't provide extraction of the entropy, just expansion of statically sized (128, 192 or 256 bit) keying material. Proving that your scheme does extract entropy well will be tough to accomplish.
The only drawback of using HKDF for this is that the keying material must be in memory to perform the calculations; you should make sure that this is (1) possible and (2) possible to secure. How big this drawback is depends on the situation.