Body and Paint Questions

My car was repainted about 14 years ago. It was a waterbase base / clearcoat over the original paint. They obiously scuffed it up and used primer, however about 5 years ago I was hit in the drivers side quater and pretty much quit washing waxing driving caring for this car. The clear coat started peeling off as it sat in the sun in the same place for about 5 years. I guess I was just at a loss as to where to start on this car becouse I have lots of plans but little budget. Finnally I just said screw it and want to at least have the paint, interior, vynal top and glass in by the summer, engine will come later. So I talked my brother in law to helping me fix the quater, I scored a new rear valance from a wrecking yard and started sanding.

My goal was to get the clear coat off as it was flaking in many spots. I have sanded through the clear colar coat and in some spots the primer and original paint, down to bare metal in some places.

Couple of questions:

Are these high spots where I have sanded through to metal?

If so, what primer can I use that will bond to the metal and the paint, I know this is probablly dependant on the type of paint I use (single stage or base/clear)?

If these arent high spots and I just sanded too agressively does this mean I need to go to bare metal?

My brother in law is good at body work but he's not a "painter" although he does paint a lot at the bodyshop that he works at. He ususlly shoots single stage as thats what they use on the Diesel Trucks that he works on so he dosen't have all the answers about car paint, in fact they use a lot of rattle can primer there. I do trust his work enough to shoot my paint, he has an Iwata gun and we will be borrowing the booth at his body shop.