1. You could be talking the Climb Skill (STR, Armor Penalty, move at half your speed) or the Acrobatics (jump) skill (DEX, Armor Penalty, no movement penalty). Climb is pretty easy so your fallen pillar could be 90' tall and all it will take is a few rounds to get over it - each successful climb check they get closer to the top. Jump has much harder DCs to get over vertical obstacles, and if they fail they don't end up partway over it so they either make it or fail entirely and have to try again next action (they could try twice per round). Strong characters are more likely to succeed at climb, Dexterous characters are more likely to jump. Climbing means that if the pillar is 15' tall, most strong characters can get over it in one move action unless you make it very smooth or wet (or both) to make the DC very hard. Jumping is much harder, a 5' tall pillar already requires a 20 DC to jump over it, a 10' diameter pillar lying on the ground would require a DC of 40 to jump over.
2. Take-10 is almost always allowed. A long jump of 8 feet is just DC 5 (or DC 8 if you read the table liberally - the DCs are actually 1/foot of distance, but they're in 5' blocks; I like to be more granular so I just use 1/foot of distance, this way a 9' gap is harder to jump than a 5' gap). That means anyone who doesn't have a penalty can, with a 10' run, jump across them easily. Without a 10'run, they need a DC of 10 or 16 depending on how you read the skill. If you want to make it more challenging, have the floor covered with rubble (+5 to the DC) and have so many cracks that there is NO way to get a 10' run (double the DC) so that even a 5' crack has a DC of 20 to jump across. But beware, cracks like this can be fatal for a failed jump, and a strong but not dexterous fighter/cleric wearing cumbersome armor will usually have a big penalty and die easily - so make the falls fairly short if the PCs are low level (and if not, then spells like levitate or fly can ruin much of the fun anyway).
3. You set the perception DCs to whatever you want. A good rule is that setting the DC = to their level is easy, = to level +5 is common, = to level +10 is difficult, and = to level +15 is very hard. Also, a falling pillar should be considered a trap, so characters who look for traps can use those class abilities. Dwarven stonecunning should help too.
4. Cover is pretty well defined in the combat rules. There are two kinds. Cover, and Total Cover. A wall half your height provides regular cover (+4 AC). In order to get Total Cover there has to be no line of effect or line of sight to the target. The books examples really only use horizontal measurements for Total Cover, but the same concept works vertically. Clearly, a guy who is a foot taller than his obstacle can be seen and targeted, so he does not have Total Cover. Also consider "Improved Cover) which is a +8 bonus (instead of +4) and applies when the creature is almost in Total Cover but not quite - it's up to the GM, but you might apply it when only the top of a targets head is visible over a tall object. None of this is any different for alchemist bombs (or other lobbed objects) - it's the same rules for all attacks.