So you're close. Here's how it goes.
Joe is a human with 2 in all physical attributes. This means his natural maximum is 6 and his augmented maximum is 9 (6*1.5 round down SR4A 68) in all of his physical attributes (Metahuman Attribute Chart SR4A p. 81).
1.) If Joe buys Muscle Replacement 4, his Strength and Agility become 6 (2+4) and he's fine. If he spends 15 karma to buy his strength to 3, the total is now a 7.
2.) If he buys a normal cyberarm, then the arm's attributes are Body 3, Agility 3, Strength 3. He can buy enhancements to increase these values. Each increase uses Rating in capacity. So for example if he got Strength Enhancement 3, his new arm's statistics is Body 3, Agility 3, Strength 6. The enhancement uses up 3 capacity. He can only go up to rating 3 enhancements though since he only has a meat torso.
3.) Joe gets a cybertorso. Now, he gets a normal cyberlimb and gets Body 1, Agility 7, Strength 7 enhancements. You would think this gives him Body 3, Agility 10, Strength 10. However 10 is greater than his augmented maximum of 9 so his arm's Agility and Strength are 9 not 10.
3a.) Our friend Joe decides to get Genetic Optimization (Agility). This increases his natural maximum by 1. His agility's natural maximum is now 7 (6+1). His new augmented maximum is now 10 (7*1.5=10.5 round down). If he has the cyberarm from 3, his agility is now 10 not 9. His strength is still capped at 9 however.
4.) Joe now looks into customized cyberlimbs. He can buy up customization levels. This allows him to buy up the values of his cyberlimb up to his natural maximum i.e. 6. So he gets a Body 6 Agiliy 6 Strength 6 customized cyberarm (that's an extra 13500Y and +9 avail to the cyberarm) but all of this uses up no additional capacity.
4a.) If he got Genetic Optimization (Agility), then he could customize up to Agility 7 (his new agility natural maximum).
5.) With his fancy new Body 6, Agility 6, Strength 6 cyberarm, Joe decides to buy some enhancements. Buying Body, Agility, Strength enhancements 3 uses up 9 slots and gives him Body 9 Agility 9 Strength 9. Even if he gets a cybertorso, he can't go any higher since 9 is his augmented maximum. If he somehow got an agility augmented maximum of 12, then he could get Agility Enhancement 6 and have an agility of 12.
On a related note is cyberlimb averaging. If you're doing a test that only uses a limb (such as grabbing something or attacking with a cyberarm), then you only use that limb's attributes. A partial limb's attributes only are used for this sort of tests, not for any other. If you're doing a test that requires careful coordination of several limbs (such as running down a hallway uses both your legs), then you use the lowest of the attributes of the limbs used.
For everything else (such as resisting damage), you average all limbs together used in the test (round down). Now technically there are 6 limbs for most metahumans (head, torso, left arm, right arm, left leg, right leg), so you add all them up and divide by 6. However very few people follow this including whoever wrote the cyberlimb example on SR4A page 343. There's a couple of different ways you can read this. The way that seems most common (at least I haven't seen much QQ over it) is to have the head count as a partial limb (and thus not averaged) and average the other limbs together (so torso, left arm, right arm, left leg, right leg).
So if our buddy Joe has an body 7, agility 5, strength 9 arm, he rolls different amounts depending on what he's doing. If he's shooting a gun, he uses his arm's agility of 5. If he's doing something that requires careful coordination of the arms, he likely uses the lower of his two arm's strength value or 2. If he's being shot he averages his limbs together (Body 7 arm, body 2 arm, body 2 torso, body 2 leg, body 2 leg) and gets 15/5 or 3 so his effective body is 3. Now when you average or use the limb's value, or the lesser of the values depends on the GM since the guidelines are so vague.
