dropping the headliner is very easy on a civic. it's one big piece. the moon roof motor is right in the front and easy to replace when the headliner is removed.
you can acquire a motor for a cheap price. as for the track being broke. you'll have to replace that piece. removing the glass isn't that hard, I myself have not done it though.
You also have to be careful welding on the roof. it's like the welding on the door skins. very thin metal too much heat and it'll warp.
if I were to remove my moonroof. I would put in a new roof all together. More money, but I'd feel better about it.