I have a few questions please guys;

Headliner
I managed to get the headliner off, seems like there was a couple of screws I didn't spot as I only removed the rear plastic trims partially, will I need to repair around the screw holes for the roof to be supported properly? If so any suggestions with what?

Pillar Trim
The drivers side trim wasn't flush so I removed it to see what's going on, There seems to be a black stuff near the corner & over one of the clip brackets, I'm guessing this isn't standard and that there has been a repair of some sort, shall I just remove it to see how the trim lines up? And is there anyway that water would of got in resulting in the headliner sagging, would it be worth running a silicone bead around the top of the window now the trim is removed, or is there just no way water can pentrate inside and the sagging is down to age?

Drain off beads on roof
They are in quite poor cosmetic condition, is it worth sanding and repainting with spray or touch up pen or best just to buy replacements?

Thanks in advance I appreciate any responses.