His writing is so confusing that it's difficult to make out

make out + 宾语从句 what it is he is trying to express
本来这个宾语从句应该是 what he is trying to express
这里在what 后面加上 it is (that) 构成了,特殊疑问句,或者更准确说是 从句的强调句型结构.
我觉得这里应该加that比较好!
类似结构 where are you going 改成强调 where is it that you are going?
I don't know who you are.改成强调 I don't know who it is that you are.

这个句子容易误解。
what it is作make out 的宾语，作为一个名词概念，同时又被he is trying to expressed这个定语从句修饰。
很高兴为你解答！
老师祝你学习进步！
请及时采纳哦！多谢你的问题！^_^