So based on what you have said:
1. Problem started after 1mz engine swap.
2. Problem was happening both before and after new clutch fitted, pressure plate fitted and slave cylinder.
3. I'm assuming the master cylinder was the first thing you checked and have no loss of fluid or leaks.
4. Clutch lines are definitely not near the exhaust.
5. Bleed and filled new fluid twice so definitely no air in the system.
Based on all that I don't think you're boiling clutch fluid. The only thing that can boil it is the exhaust and being NA probably still doesn't get hot enough regardless.
I don't know much about 1mz engines but I was trying to see on the internet if they have a pilot bearing. From what I could find they seem like they do depending on the year. Was your pilot bearing changed if you have one? Possibly it is seizing when getting warm. Do you get any noises when engaging or not engaging the clutch? Could be something around that....I'm just guessing though because I can't think of anything else.