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...
Were here can be translated as:

* 本来有

Making your sentence something like:

（这儿?）本来有两个不好的部分

---

* 有了

Cannot expresses "were," the only thing it can express is `(I) **now** have sth.` & more specifically: (I'm) pregnant.