after what seemed a long time （正）

结构正确，语义也正确。after 是介词，后接包括名词性从句在内的名词或名词词组。

1. 因为what 是融合性关系代词，所以：after what seemed a long time 约等于： after a long time又如：He lives in what seems like a hut. 约等于：He lives in a hut.

2. after 用作介词时，可以接：时间点；时间段。

after three o'clock：在三点之后

after three hours：过了三个小时之后

例如：

The meeting began after three o'clock, and after three hours, it was over.

会议在三点后开始，过了三个小时后，会议结束了。

然而，用作连词， after 只表示在一个动作结束之后，例如：After the guests left, they went to bed.

但没有第二种用法（即：没有“经过了多长时间之后”）。说明下句是错误的。至少是逻辑错误：

after it seemed a long time （误）

这里after 用作连词。结构正确，但语义错误。after it seemed a long time 跟以下句子结构上没有区别，简直不敢想象它们是什么意思：

After this was a book, ...

After she was a girl, ...

After it was a long way...

After it was Sunday...