This is old I know but here is my own two cents into the argument:
Since a person can also have digigrade legs installed we have the nail in the coffin of replacement theory because digigrade legs increase "the running speed multiplier... by 1 for each pair." (CF 87) which very clearly indicates that the leg is determining the AGI that speed is calculated off of.
Actually, all it means is that a runner with a dump stat of AGI 1 is running at 5meters/round. (asuming 2 legs) It doesn't offer proof that the cyberlegs AGI is used.
The German version of Chrome Flesh clearly settles on the side that inherent limits and movement is based on the STR/AGI of the runner and not the cyberlimbs. And most (but I'll allow for some detractor out there) would agree the German versions of the rules are better than the English... albeit you need to be able to read German to use them. But for those who don't like the way cyberlimbs are treated in the current edition, the German rules offers an optional rule: the cyberlimbs effect inheret limits and movement for those who replace all 4 limbs.
In any event, Chrome Flesh offers another partial solution for the people who want to go AGI or STR 1- it's called Redlinner While it has it's drawbacks it increases the characters actual STR/AGI. So someone with STR 1 and 4 cyberlimbs would become STR 1(3) thus increasing his phsical limit and AGI 1 now be using 1(3) to determine movement,
Well it actually does still indicate that it's a replacement as its the leg (with digigrade legs mod) that is determining running speed, where if you get it in a real leg it modifies the real leg's rates and if it's cyber it modifies the cyberleg's rate. (As mentioned, you "replace" the limb ergo you replace the stat, you could still argue running is full body but you are still using the cyberleg agility with whatever else you are averaging.)
The houserule actually then settles the debate (thank you german version) since this thread was started with the question of "if i have replace all 4, how do i math myself?" Saving this link for later...
Redliner, I am fairly sure, would still apply to the cyber limbs as it's mechanics imply that you are weakening you cyberlimbs by overtweaking meaning you are tweaking said limbs as well as possibly your own body in other ways. Also, overly nitpicky but by super hardcore reading "per two full cyberarms and legs" would mean you only lose 3PC after you have replaced the full 4 limbs. That said, if you have the cyberarmor to cover the loss, it is a niceway to save two capacity and actually make cyberlimbs reach that Max+4 limit.