Since they are specifically mention to be shells rather than replacements...
Despite being a shell rather than a limb; both skull and toros are still Cyberlimbs, they are still listed in the Cyberlimbs table and still use Cyberlimbs rules.
(unless a more detailed rule say so; melee cyberguns for example can only be installed in cyberarms. That mean you can not install them in cyberlegs, cybertorso or cyberskull).
...do you use their attributes to calculate limits when using them for a test, either individually, as an average, or as the weakest limb?
There are 3 options here. It depend on the test.
1) Shooting a light pistol use the agility and strength of the arm and the limit of your weapon even if the rest of your body have higher or lower agility, strength or physical limit.
2) Shooting an assault rifle use the average agility and strength of your left and your right arm (round up) and the limit of your weapon even if the rest of your body have higher or lower agility, strength or physical limit.
3) Using your arms to lift something really heavy from the ground use the weakest rating of your right leg, left leg, torso, left arm and right arm. Since this is an attribute test there is no limit so for this test it does not matter what your physical limit is.
Q: Is surprise a situational event...
Yes.
If there is a surprise situation it is most often at start of combat but combat can start without anyone taking a surprise test. GM can also call for a surprise test after combat started.
Q: What does being Unaware of an attack entail...
Defender does not roll reaction + intuition when defending against an attack. If defender is behind cover then defender roll a total dice pool of 2 dice for 25-50% cover or 4 dice for >50% cover.
...and when can it occur?
When defender is unaware of the attacker. For example melee successfully sneak up behind the character before combat started, Ranged attack from behind, Sniper from far far away, Defender can't see the attacker due to total darkness or being fully concealed behind cover.
A surprised character also fall under this category but only against targets he is surprised by.
...characters in cover gain a defense pool equal to the cover, +2 or +4. How should this rule be interpreted?
A character that is unaware of the attacker (see above) will not roll reaction + intuition when defending against an attack. He does, however, still roll a total dice pool of 2 dice if he got 25-50% cover or 4 dice if he got >50% cover.