The fact that the clock can only be activated during a lunar eclipse makes a lot of symbolic sense. The phases of the moon are one of the oldest methods of measuring time, so it makes sense that a spell designed to distort time could only be activated when the moon is disfigured.
The Omega symbol is repeatedly shown to be associated with Isaac. This may explain how he was able to get past the horseshoes nailed to the front door - horseshoes are shaped like the Omega symbol, hence would not be as effective against Isaac.
On that matter, the protective measures were likely less effective because they forgot to take the house itself in account, and the house isn't good or evil, just loyal to its original owners (as shown when the mirror matches Isaac's being raised despite the protections still being in place). The pumpkin themselves are actually part of the house, as shown by the griffin topiary, so of course they won't do anything against its owners, and the horseshoes are likely supposed to keep out evil creatures, not human beings with evil intent. Notice that Selena merely ignores them, but Isaac, who's a zombie at that point, takes them out and burn them before entering, suggesting that they do have some effect on him.
The Izards' plan required a very specific person to use as a patsy. They needed someone whom Jonathan would let into the house, who was innocent enough to get through the wards around the book of necromancy, who was powerful enough to cast the spell calling Isaac back, and who was ignorant enough that Selena could dupe him into casting it. In fact, those criteria are so specific that Lewis is almost certainly the only one who fit them. It certainly is lucky for the Izards that Lewis's parents died when they did, just long enough before the lunar eclipse for them to pull off their scheme... Was it really luck? Or did Selena kill Lewis's parents to ensure that their scheme went off?
For that matter, the scheme also required Tarby to befriend Lewis, turn against him enough that Lewis would want to impress Tarby with magic, and then get it into his head to open the forbidden cabinet and take a look at the book inside. How much of Tarby's behavior was him, and how much was the result of Selena's tampering?
Possibly Selena broke Tarby's arm.
Actually, in his first dream with his "mother", Selena was already trying to get him to unlock and, possibly, use the book on his own. After the book was out of the cabinet, Selena could have done everything else by herself.
There is also the possibiity that Isaac did not expect to die or that his house would have been taken over and the book hidden, and made everything else on the fly. After all, if they planned that all along it would have made more sense for Selena to prepare a fake corpse and not come at all, instead of just running to another room and hiding there before sneaking out.