Question:

I'm finding it incredibly hard to organise transportation for my trip, I am planning on going from Tehran and catch the night train to Isfahan and then catch another night train to Yazd and as far as I'm aware I cannot catch a train to Shiraz so I'll have to catch a bus and finally catch a plane back to Tehran.

Answer:

For the information and reservation of the transportation in Iran you can check: Iran transport services.
And check the cheapest Iran tours.