If the attacker targets a specific location (+4 TN), the first two successes go to hitting the targeted location – if less than two successes are achieved, roll on the above chart. Any further successes stage the damage up as normal. If damage is coming from a burst-fire weapon or an area explosive, make a separate location roll per wound box sustained, with each location rolled taking one potential wound box worth of Stress.
For each wound box of unresisted damage sustained to this location, each piece of cyberware or bioware attached to the organ system rolled checks for one point of Stress. Thus, if a character took a Moderate wound, and rolled a 6 and a 3 for hit location, the character would check for Moderate Stress to each lung-based cyberware or bioware –Extended Volume, Air Tanks, Gills, or the like. If the character took a Serious wound, and rolled a 3 and a 6 for the hit location, he check for Serious Stress to any cyberware or bioware in his Left Leg – a cyberlimb, muscle augmentation, enhanced articulation, bone lacing, or any other such system.
The Stress Check is performed by rolling one die per wound level sustained against a target equal to the original Power of the attack; any dice that do not come up a success are applied as a single point of Stress to that organ or system. Thus, a character hit with a 9S attack, who stages it down to 9M, would roll 3 dice against a target number of 9 for each affected system, with each success reducing the amount of Stress for that system by one point.

Trash all the old values and make up new ones on your own. Do NOT start calculating any new values from the old Armors, it will not work. Make up your own values, and it might. I'm not saying Hit Locations are great, or even that they work great, but I am saying that the problem TinkerGnome mentioned isn't really a problem at all if you're willing to spend some time with it (an hour or two should do it).

More on the topic, I don't think it is a good idea to be using a Hit Location system for Ware stress without using Hit Locations and armor rules to go with it, since breakdowns of logic will follow. And if you've got a Hit Location system already, you don't really need another one to figure out Ware damage. I use HitLocs, and then apply common sense for Ware damage. Ie. if there is a possible wound effect from damage, it can only affect ware that are located where the char was hit.

If you don't plan on using HitLocs for other purposes, you're probably better off using the rules as they are; and if someone gets Stress in his/her Suprathyroid Gland as a result of getting hit by a bullet, then that's where the bullet hit.