This came up in our game last Sunday.

If a stationary target has Partial Cover (+4) (SR3 p. 111), or 50% Cover (+4) (CC p. 97),

and I take a Called Shot with a chemical delivery weapon (M&M p. 106) to a limb in that 26% to 50% of the body that is fully visible,

and Smartlink-2 modifiers apply (+2 for Called Shot),

do I ignore the Cover modifier?

Not in my game.

Realistically speaking, and the way we've been doing it, if you make a called shot to an accesible body part, you take the penalty for the called shot not the cover. The body part isn't covered, ths the called shot...otherwise, forget about taking a called shot, and go for a normal hit. There has to be a certain sense of logic. If you think it's too easy for the called shot, modify the TN or give an extra die for DODGING because they have cover. But stacking a cover and a called shot penalty defeats the point, and demoralizes the character doing the shooting.

You'll be much better off if you just go with the BBB logic and decide that a Called Shot doesn't really mean it's going to a specific body part, just that it's better aimed in general. And it's harder to aim better if someone is in cover. Then there's no question that they stack.

Actually, even if you use the FAQ-logic, you still don't really get to call a shot to a specific body part, only some more specific effects. So there's still no reason to allow someone to get rid of the cover modifier because they call a shot.

You should search this forum and the old one for this, but here's at least one more argument that I can remember from the earlier threads on this:
Cover doesn't really mean that you are just sitting there with one part of your body constantly visible and the rest not at all. ~90% cover might mean that 1/3rd of the time the enemy can see 1/3rd of you. Thus you can't really call a shot at what's visible, because the same things are not constantly visible -- indeed the guy might be totally behind the cover for a significant portion of the Combat Turn.

So let's say that Wiz, who has Pistols at 4 is going to shoot at that annoying security guy who's hiding behind his desk and is going for the PANICBUTTON. Wiz has an angle that lets him think he's got a chance to shoot the guy in the shoulder and make him think twice. Wiz aims and fires. It should break like like so.

Base TN: 4
Range: Short (electronic vision mag) no mod
Light: Low lighting, natural thermo +1
Called shot: +4
Smartlink: -2
Aim: -1
Wounds: none taken, no modifier

That would make Wiz's TN to hit 6, so he rolls his dice, and get's three successes. The GM decides that the security guy is going to try to dodge...so he rolls whatever Combat pool he has left, and decides that the cover is going to drop the TN to dodge by 2 (1/2 the normal cover rating). So the TN goes from a 4 to a 2, and the GM rolls the 4 dice from the combat pool.

This seems to be the most realistic way to do things, atleast to me.

That seems like a reasonable house rule.

BTW, Electronic Vision Mag wouldn't work with a Smartlink anyway, so the mention of it in the Range-section might be a bit misleading.

Yes, you add in cover to the shot.

Cover represents someone moving from and back behind cover, not just standing statically like a target. You still have to contend with that when making a called shot. Assuming that people are just standing still with half their body exposed is pretty silly.

All arguments about what a called shot does or does not mean, I'd say take it literally and rule depending on the sitch. If the guy is hiding behind a low wall and you can see his head and gun arm, and he's reasonably static, then a called shot to his leg isnt going to work, now is it? if he's dashing about between low walls though, I might rule called shot is indeed impossible unless you spend a while observing to see if there's a pattern to his movement and line up a shot where you think his head's going to appear in a second or so, making the called shot then.

The rules are abstract because you can't legislate for every occurrence. However, players don't work that way - how are you going to explain to a player that 'called shot' doesn't actually mean that its a specific thing you're aiming at, even though it means exactly that if shooting at part of a vehicle? that's using the rule differently in different situations for no readily apparent reason. Partial cover doesn't mean they are static, but I'd certainly say that it means roughly the same percentage of them is covered at the same time. Common sense. Don't worry about getting it exactly right cos any player sat there with a calculator working out if your target numbers are wrong on a regular basis probably deserves that sniper rifle round you've been saving for three campaigns just for being an irritating prick...

If you allow people to use called shot on partially covered targets without the partial cover modifier even without smartlink 2 you have pretty much eliminated partial cover from the game.

There is no reason not to call a shot if it is possible because the target number is the same (or lower with the cursed sl2) but the damage is higher. The only constraint is the need for a free action to call the shot, so about half of the shots against partial cover in the game should be called.

Like several people have said SR combat is abstract. Try to change that and you have to change everything.