Question: I'm trying to construct a sentence along the lines of, "There were two hard parts...," where I use the existential 有. The issue I'm having is how I convey the meaning that this 'existence' is confined to the past. Should I be using the perfective aspect 了 like:

有了两不好的部分。。。

Or should I include some clause afterwards to indicate the new state of things:

有了两不好的部分。。。现在都没这部分了。

Or is there some other way to do this that I'm missing?

Answer: 
I'd suggest you adding some time information in the front to emphasis the fact it is in the "past" as that is definitely unambiguous. 

* **以前** 有兩個不好的部份...
* **之前** 有兩個不好的部份...

Alternatively, these ones can also be used. They means "originally", which implies "in the past, and now changed"

* **原本** 有兩個不好的部份...
* **原來** 有兩個不好的部份...
online dictionaries have examples, e.g. submit "there were" to iciba: "there were" 我们学校曾经有许多树 suggestion:曾经有 (非常困难的部分 hard parts, also from iciba)), to see whether 有了 is possible check iciba's examples for 有了 (of course "have become pregnant" comes to mind) 丈夫有了外遇、有了取得进展的迹象、飞机的念头在参军之前就有了，conclusion 有了 conveys sense of something having happened

according to users' memory there is a previous question
containing info about verbs that cannot be followed by completed action marker 了 （有 among them with exceptions), but so far unable to find it, the following may therefore (inadequately） duplicate previous answer) <https://app.ninchanese.com/stage/grammar-lesson/43/56>
Verbs that describe a state, (in case of a change to a new state 了 may occur, see above 有了 or 知道了，learned）

previous Q&A has been found see [Which verbs DO NOT go with 了 and or 过?](https://chinese.stackexchange.com/questions/20856/which-verbs-do-not-go-with-%e4%ba%86-and-or-%e8%bf%87/20857#20857) esp comment#2