As Neil and you have shown in the comments, you're not using the right construction here. You are trying to use it as a dummy subject, to be picked up by to make clear. But that is only possible in English with words that cannot take an infinitive themselves:
It's better to make these issues clear.
Here, the dummy subject it is picked up by the subject complement, which is the infinitive plus dependencies: to make these issues clear. It is possible because better doesn't take an infinitive itself, so that there is no cause for ambiguity. It means "making these issues clear is better".
It's needed to make these issues clear.
Because needed can take the infinitive, the same construction is not possible here. Readers will take needed as governing to make..., as you said. The sentence then means "this is needed in order to make these issues clear". That is why you need to cut needed loose from the infinitive to get the desired reading while keeping the infinitive, as Neil suggested above:
What is needed is to make these issues clear.
This means "making these issues clear is needed".