1.) 通過予定[つうかよてい]タイムを５秒オーバーしてるわ
I think it's something like,
You passed (the checkpoint?) with 5 seconds delay. or
I was expecting you to pass (the checkpoint?) 5 seconds before (the time you actually passed).
3.) ミシェルの位置かバラけてるわ アヤ ちゃんとリード なさい！
Aya please clearly report Michel's position or condition!
The game controller wants a report on how this team is doing.
--Here I don't really get「ミシェルの位置がばらけてるわ」。The speaker may be saying that she can't see where Michel is. Then 「リードしなさい」may mean, as you say, ’report her position! (by following her)', or 'put her in the right position (by leading her).'
5.) 彼の間合いのギリギリを頭に叩き込みなさい!
「頭にたたきこむ」=to beat something into your head.=to learn/memorize something perfectly.
「間合い」=the right/suitable distance/interval.
「ぎりぎり」I don't understand how the word 「ギリギリ」can be used as a noun. Here it is used as the object for the verb 「叩き込む」. It describes a state where something is very close, means '(being on time) at the last moment' or 'in the last limit.'
12.) 。。。全く
... I absolutely agree
It depends on the context. It can be 'Indeed!/I absolutely agree' and also 「全くもう…(何をしているの？/あきれたな/しょうがないわねetc.）」＝'Reality, it's appaling!/Really horrible!' etc.
（Just 'indeed' or 'really' has remained and everything else has been left out.）
折角息が合ってるのに何やってるの！
＝せっかく息があっているのに、何をやっているの！
=You two were working together quite well. Don't waste it!
16.) 。。。ハズレ。
...A loser
. . . End.
. . . Disconnected.
The target ends up to be something strange and not what the group was expecting to find.
---Right. The word はずれ is exactly the suitable one for this situation. It comes from a 'blank' in 'I drew a blank.' It's like 'a dissapointment' or 'a miss.'
18.)
三＊木のPCにハッキングかけたあ？
「尋」[じん・たず（ねる）]？There seem to be more strokes...
「三尋木」looks like a family name...I don't know how to read it.
んじゃ はじめっから敵の位置もターゲットの位置もわ かったのかよ！？
Just put 「そ」on the top.
んじゃ＝「そんじゃ」＝「それじゃ（あ）」＝「では」 =Then/So
Did you know the location of the target and the enemy from the beginning, then!?
So, you mean, you knew where the target and the enemy were from the beginnig?
19.) 最短で最良の方法とったまでだよ
It is just that I took the shortest way and the best method!
でもギりギりまでこの猫だってわかんなくて追っかけん の大変だった～！
But until the last minute we didn't find out it was a cat so we had such a hard time chasing...
ターゲットは生きてるとだけ言ったでしょ
I only said, the target was alive!
All I said was 'the target is alive.'
固定観念は捨てるのね
I abandon the fixed idea, isn't that right.
---Yes, you may be right, but here again it depends on the context.
It also can be
=固定観念は捨てなさい(imperative)
(You should) Abandon the fixed idea.
A.) 「あのときは、多数決[たすうけつ]で、○○にしただけ」
The two kanji letters I can't figure out. Can you enlarge them, clearly if possible?
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As for the other parts that you mentioned and I didn't deal with up here, I found nothing wrong with them.