For the door cups behind the handles, take a soft cotton cloth and Meguiars 105, and rub the area from the top and the bottom. It is ok to use a little pressure, and keep the compound damp enough to work for a bit.
Clean out the area with a clean microfiber and see how nice it looks !

For A Pillars between the front and rear doors, etc., its a good place to use a 4" foam pad or even a 3" if you have a rotary with the appropriate sized backing plate.
Since you only have 5.5" pads, it will be harder, but not impossible. Just make sure you tape off any plastic and rubber moldings around the A pillars.
This paint here is sometimes a little fussy because the pillars are usually plastic so it heats up faster and doesnt dissipate heat as well as metal.
You can try to use a soft cotton or microfiber pad with something less abrasive, perhaps your Meguiars 205, be gentle here, its hard to say how much actual paint is on these pillars.
Flex came out with a smaller believe its 4 3/8" backing plate for using the smaller 5" pads, so that might be a good thing to think about getting sometimes, and of course some 5" pads..
I never tape body lines or body panel edges; just let up on pressure and speed when you get close to them and go over quickly. Edges are so sharp that they cant possibly ever really get dirty anyway, so they don't really need correcting like the surrounding areas may need.
Your Flex 3401VRG (I also have one of these), will be just fine in those areas.
Just try to keep the pad as flat as possible, but don't worry if you cant. I use the edges all the time to help speed up correction of badly swirled, scratched areas, but finish by going over those areas with the pad as flat as possible.
Good luck with your project !
Dan F