Thoughts from 18 year body shop experience
Lets start with the simple problem first: The sand scratches that you see in the door are most likely to be primer shrink. That is not to say that there is not body filler in this area, but the primer used to fill the small scratches from sanding the door has shrunk. This is most commonly caused by force drying the primer, to save time. This tells me that the car was fixed by a production shop and leaning toward an insurance claim at that. have you run a carfax on this car? or a accident report record for the VIN # in the area that the car is from? As far as the standard Regal header panel being used not a big deal. The old repair would have to be ground out and fiberglass repaired with mesh. The car may drive straight but I would take a real good look at the shims in the upper control arm area to see if the left and right side are close in the number or space of shims used. As long as we are on the topic of shims ... check the front body panels for shims. Fenders, hood, bumper, header, and so on. Any uneven shims from left to right is a dead giveaway that this car has issues that you do not want in reference to frame damage. When a GM full frame vehicle gets hit in the front the most common area to bend is not the front rail end, but the part of the frame rail in the bend behind the tire. Turn the wheels and check the area where the frame has the downward slope coming off the spring cup and then goes down under the driver floor, both sides. Check the car for frame machine clamp marks in the frame or tears in the frame from the car being tied down. "T" slots torn or any of the factory holes in the frame torn are bad ...period. Just because the car may look good does not mean it is a good repair. the paint job may look to be a 8.9 to you, but you are correct about what lies under it. A car that has 3 different problem areas is just that .. a problem. My last thoughts are as far as getting a new paint job goes, $3K will not cut the mustard. Just as many things " you get what you pay for" and any one that would paint an entire car for $3k is going to cut corners. that is just for the paint. not to mention the body work that will have to be done. I would say a fair estimate for repair to what you are looking for 41k miles would be $6-$8k
NOW THE SHORT VERSION: I would continue your search