When using the Custom Id for Battle Pets to hunt the rarest ones that appear in the wild. I have put in the custom NPC ID, but the alert will not trigger unless I mousover the npc itself after I've already located it. Is there a way to fix this issiue or have I done something wrong in my input?

I tried doing this today — expecting the id of a battle pet to let me scan for a rare battle pet only for it to work when hovering over it. I'd like to hope this feature is possible given they show on the minimap, if so, this would be a great feature.

The targeting macro also did not work, I believe it was mentioned in another issue that this may be because SilverDragon does not know which zone these custom mobs may be in.

I haven't checked lately... but if you're on the alpha builds it actually might work now. Since the last release build I've redone custom mobs so that you can add them globally or for specific zones, and if you do add them for specific zones then they start getting put into the more-expansive scanning methods.

Specifically, if you're on the alpha and have added your pet to the zone you're in, go into the scanning options and turn on the "dark magic" method. Crank its interval all the way down to 0 as well, for the heck of it, and SilverDragon should yell at you as soon as you're in targeting range of such a pet.

(Blizzard actively tries to make it hard for addons to know about things on the minimap, so that doesn't help. Mostly because they want to make it harder to make resource-gathering bots, but anything that's a "tracking"-type gets caught up in that.)

Okay, further! The targeting macro will now include zone-specific custom mobs as of fb0f1d4.