Just some suggestions for your consideration,
I would suggest when one removes the protector strip they focus first visual impression on how straight the flat and smooth surface compared to each panel is, how each panel lines up, also accentuates lumpy bumpy lines from the front of the guard, over and along the door and back to the rear quarter, and sightly miss aligned joints,
I see you are doing fine, and perfectly capable of preparing your car for very hot paint job whatever the colour, , bit scary at the moment, you going to be driving this car for a while, I remember how it was for me,
Please note, I would highly recommend removal of all clear coat, your clear coat was damaged and oxidizing, my line of thought is if you could visually see a lot of oxidization, there is always much more oxidation you cannot see, and it could release its adheres ion to the base colour coat later on an spoil or bubble, your paint job, I suggest now is the time to remove it, and not have to worry at all,
Ok, this picture shows red tubular shape on the floor, indicating a work light source; darker blue lines show light up to thin long stainless steel flexible metal straight edge ruler. 3 feet,??. Held against the side of the car panels with both hands, light blue arrows show you looking down at the ruler looking for light getting though gaps and bumpy surfaces, and can be used to find slight variations on surfaces all over the car,
To line up and straighten up door panel edges and corners, first Red circle, remove door handles, and door lock striker plate, and door rubber, so the door can swing freely while lining it up, and everything can and will line up, with the straight edge, you have to remove the door rubber anyway to paint inside the door Jamb,
Next is the square dark brown lines on the rear quarter hip, small boxes are off cut bits of wood to serve as handles, epoxy glue to off cut 3 foot long 6 inch wide plastic free floating floor board, second hand or new, under the board is PVA glued P600 to p1000 sand paper, 3 x 6wide strips of sand paper on end, cheap enough to make few,
While holding the handles the 3 foot long flexible sanding board is slightly twisted and bent around each contour of the each panel, the trick is not to apply pressure, just keep the board flat, all 4 corners and the middle in contact, rub a few times and wipe away the dust, and look hard at where the sand paper is in contact, a lot of thumb size high spots can be levelled or slightly indented with your thumb, or 2 thumbs from strong hands, can press in small dents in the rear quarter cause by loose cargo in the boot, the trick is to progressively increase thumb over half a dozen or 6 attempts, or presses, gradually increasing pressure, and do not push in a dent,
A few minutes of circular rubbing will highlight, high and low spots, and checking with the straight edge and light will give some indication whether the high spot can or should be removed, or low spots have to be filled, like a slight dent, to compensate for other unknown factor at that point,
Further rubbing may show areas where the original base colour is thinning on high spots and in danger of breaking through to the metal, so contact your painter and find out what under coat primer filler you can apply with a paint brush by hand, just to sand and use as filler for slightest dents, and put some primer coat coverage over thin original paint areas, this gives you the chance to have a super glassy flat finish along and over the length of the whole car, before the paint goes on, my line of thought is the key to a excellent paint job is all in the preparation, that is you, and you are perfectly capable of cheaply doing this,
Black and grey lines along protector strip holes is stiff as 4 x 2 flat wood or steel tube, with pva glued P600 and or P1000, sand the patches of putty flat and keep those lines as straight and flat as a bullet, you may even have to lay a film of putty right along all the putty patches, to get it absolutely straight, because I am always checking the straight edge,
Small purple circle at base and corner of door shows the corner has perhaps been scraped on a grass bank, and could be bent around by a strong right hand into place and fit perfectly,
Larger purple circle shows wide gap opens more at the top of the door, possible from banging on a fence up high and on that point, when being closing, also please note if the s/s straight edge was used along the green line, could indicate the panel parallel to the green line has a slight kick out, so I would open the door and flat bang the corner with the palm of my hand, while closing and opening the door to check the gaps, as well as checking with the straight edge, , this will return the green line kick to zero, check again with s/s straight edge and light gaps passing between the straight edge and the panel surface, , and check again with the flexible sanding board, maybe have a little sand a minute, then check with straight edge again,
Next picture again shows light shining up under the straight edge, while I move the straight edge around and find a slight depression, I use a carbon pencil to mark the depth of filler required, and perimeters of the depression, ( I placed black circles anywhere, just to indicate how the pencil can be used and might look, ) as shown in circles which does help heaps when having to remember how much putty to mix, and the width of applicator of which plastic applicator to use,
I have and use 4-5 plastic applicators different widths, I mix putty on a hand held mixing table, with a small width applicator, then use the small width applicator to transfer enough putty to the correct width applicator, on vertical panels I find wiping the putty into a slight depression is best done vertical direction, but everyone to their own preference,
Black arrows might indicate possible oxidized top coat,
Purple circle shows gap in door opens just slightly, perhaps the car was reversed with the do open just enough to twist the door on the red arrow, bottom door hinge, perhaps bumping the bottom hinge, yellow arrow, direction, will close the gap, but suggest you might use and continual check the straight edge over the mud guard, shown by purple arrows,