[3]-If Nael or his dad had been involved, then I don't think the first project would've gone badly. I agree with Niiro's post above: Darnus Sr. probably knew more about Meteor than he told the Empire, and Nael rose to power after offering to divulge what his father knew. Would explain why he became the favorite of the Emperor and why nobody cared when he publicly executed his father's loyal men. This would sort of answer [2] too: the Citadel probably didn't belong to House Darnus if they weren't involved in the first project.
[4]-Now this is a pretty long shot and it sort of builds off Rocl's theory, but.. to control Dalamud's fall you need two things: the lunar transmitter, and runestones. Maybe the runestones are sort of a "map" which give a specific path to Dalamud, so you'd need runestones which map the area you want to destroy. This would explain why Dalamud's beam was directly shot at Bozja (which contained allagan runestones plus the transmitter) and why Darnus seems confident in being able to control Dalamud in 1.0 (he's gathering Eorzean runestones via Roclwena).