Welcome to the board Abe (when I play the Americans I'm Thomas Jefferson usually, or else Teddy Roosevelt)....
Anyway, as for scoring, I'm not sure what you mean by "bonus": is there one? All I know is, you get 2 points per happy citizen, one per content, and nothing for the unhappies. Then you get 20 per wonder, 5 per future tech, and from 100 to 400 for your spaceship (depending on how big you made it). You get penalties for polluted squares in your territory, and either a penalty or bonus for how hard you set the barbarians. As for the peacetime thing, I'm not sure how that one works exactly (anyone?). But other than that, I've never noticed a "bonus" on top of those things.... If your talking about the percentage rating, I'm not all that sure how that works either (again, anyone?), but I think it has partly to do with your level of difficulty (you seem to get a higher one with the same raw score on a harder level).
As for city walls: Cannons work fine against phalanxes behind walls. Musketeers, no dice. But you should know that if you send dips to sabotage the walls, that they will usually destroy every other improvement in the city first. And since dips die with each sabotage, you may be going through a LOT of them, and when you do capture the city every improvement will be gone and you'll have to build them all again.... Which is why I usually don't go conquering much until late game, when I can bomb the cities first (or hit them with battleships or, way later, howitzers). With spies, you may have more luck with the walls (you can choose to try to sabotage them specifically), but you're more likely to get captured before you can do them (walls are particularly guarded against sabotage). If I do conquer earlier, though, I usually go for bigger cities WITHOUT them if that civ has gunpowder. But midgame, I'm more in a building/consolidating phase. If I'm at war then, it's mainly defensive (all my frontier cities generally have walls)--meaning I let them beat themselves up against my own walls, or go around picking off offensive units with weak defenses, like catapults and elephants, when they're in the open on the way to my cities....
