I cant help but LOL at your commoner's common sense for teh feedback, well it is not your fault if you don have the firearm and explosives knowledge:

First paragraph:

1. The shot which kena Aria's chest ==> bullet force transformed into a sledge hammer(by her bulletproof seifuku) punched to her chest and make her fall into a blunt traumatic shock/temporary disable/interruption on blood circulation and thus some sort of fake cardiac arrest.

2. Why the Lupin IV did not finish her?: cause she is waiting Aria's hidden true potential to be revealed and to enjoy a fair fight in the name of Lupin and Holmes.

3. The injection works like adernaline to force the heartbeat to be active again(by chance only), from the beginning, Aria did not receive any wounds from gunshot, just blunt force trauma taken.

4. About the bulletproof cosmetic issues, so far the fabric which is designed for bulletproof vest is Kevlar/Aramids fibre. I am much more surprised that Butei students are so well-equipped until such level. The Kevlar materials used to adapt the texture of Seifuku is not easily done and it cost a lot of money for sure, I bet Butei's fees sure cost you a leg/kidney to get that level of quality.

Conclusion for first paragraph: It is logical, but not financial-feasible.

2nd and 3rd paragraph:

1. It is possible, by placing earplugs, well-placed spalling explosives designed just enough to perforate airplane's body material, nearby user will not suffered the shockwave from the explosion as the direction of explosion is designed to project outwards instead of towards the user. This can be done depending on one's expertise on explosives and extensive studies of materials spalling properties.

2. The seifuku-transform-into-parachute did surprised me a bit, but I given it up due to, it is fan service afterall~~

3. Depend of the missile type, those missile was made to punch some holes on fuel tank and engine wings instead of making the wings/engines explode. So it is logical.

4. If Butei high school got such financial and logistic ability to provide students Seifuku made of Kevlar fabrics + any vehicle for driving anytime, I guess filling in an empty space with spotlights is rather easy for them.

5. Jumping from the heli at such height, with Kinji as cushion, shouldnt be a problem for landing LOL.
P.S: Sorry for the ranting, it just that I thought all of these is possible to be exploited by logic, just that it is not financially feasible and require almost perfect planning and execution. For common sense wise, it is hollywood-alike but in fact better than hollywood in term of consistency.