试答如下：

疑问1：in the way in which,凭什么是介词in？介词 +which等于that。介词+which中的介词应该是根据定语从句中不及物动词搭配的介词决定的。如果是及物动词就用that。

在way之后跟有定语从句，而way在其中充当状语时，共有三种表达方式：(A)the way，(B)the way that，(C)the way in which （这里选in主要原因是the way的缘故）

最常见的表达方式是(A)： 
 　　　　1.That's the way she spoke.(CGEL)　那就是她说话的方式。 
 　　　　2.He doesn't speak the way I do.(LDCE)　他说话方式不像我。 
 　　　　3.People liked the way he wrote and so he went on writing.(Walpole)　人们喜欢他的写作方式，所以他继续写。 
 　　　　4.They didn't do it the way we do now.(Hill)　他们没有以我们现在的方式来做那件事。 
 　　　　5.The way she spoke hurt me.　她说话的方式刺伤了我。 
 　　　　6.No one...can understand the way I miss Dave.(F.Buldwin)　没有人能理解我是怎样地想念戴夫。 
 　　　　偶尔也采用表达方式(B)(the way that)： 
 　　　　1.That's the way that he did it.(CGEL)　那就是他用的手段。 
 　　　　2.I don't like the way that you laugh at her.(LDCE)　我不喜欢你那样嘲笑她。 
 　　　　3.They didn't do it the way that we do now.(Hill)　他们没有用我们现在用的方式来做那件事。 
 　　　　表达方式(C)大都用在较正式语体里： 
 　　　　1.She was pleased with the way in which he had accepted her criticism.(Bennet)　她对他接受她的批评的方式很高兴。 
 　　　　2.We admired him for the way in which he faces his difficulties.(Worrall)　我们因他对待困难的方式而敬佩他。 
 　　　　3.What's the right way in which to address the Queen?(LDCE)　怎样称呼女王是正确的? 
 　　　　4.One's character is defined by the way in which the rules are embodied in one's behavior.　一个人的个性可由他行为中体现的准则来表示。 
 　　　　5.The way in which this matter can be used depends on its properties.　这东西怎样用取决于它的性质。

疑问2：They did as I had asked不全的话：They did as I had asked they had done.那么省略的话应该是They did as I had asked they had才对。

补全是：They did as I had asked they should.

用法见Macmillan English Dictionary 2nd Edition

ask that someone (should) do something: The committee has asked that this scheme be stopped for now.

疑问3：Leave the papers as they are.这句they are到底是什么成分，为啥没有they are不接表语、状语？

as they are方式状语；这里are是不及物动词，用法见《美国传统双解》：

To remain in a certain state or situation undisturbed, untouched, or unmolested: 处于，持续：保持某一种状态不受干扰、没被触碰、没被干涉妨害：

    Let the children be.    随这些孩子们去