The simulation results reveal two important issues. First, X is a positive number. The second, Y is bigger than Z.
In those sentences there is a couple of places I'd make a change. First, it's OK to use "issues": one of the meanings is "result", "outcome". However, with revealed, issues are assumed to be pre-existent, and that points to their meaning as problems rather than results or outcome of the simulation itself. Perhaps you ought to actually say "results", or rephrase the first sentence and write
The simulation leads to the following conclusions.
Then, there is the beginning of the last sentence. If you start the second with the word "first", no article, thus making it essentially an adjective, then it is advisable to do the same in the sentence that follows:
Second, Y is bigger than Z.
Now, to your questions.
A1: No, if you use "first", then drop the "the" for "second".
A2: You can use "results", "outcomes", or rephrase to avoid using "issues".
A3: I am not sure it's better, but it might be a bit cleaner/clearer:
The simulation results point to important conclusions. First, X is a positive number. Second, Y is bigger than Z.
As you can see, if you already use "first" and "second", perhaps there is no need to announce the number of conclusions.