Resealing headlights is as simple as gobbing more silicon on them.
As for replacing the projector, the limiting factor is the (usually) small size of ebay projectors. E46 projectors consequently are recommended for this since they're smaller and fit easier.
I think these look better than OEM or even professional retrofits in terms of sheer aesthetics:
eBay Motors: 06 07 HONDA CIVIC 2DR BLACK HALO PROJECTOR HEADLIGHTS (item 190214174963 end time Apr-16-08 22:11:04 PDT)