Great video Glen. Appreciate. Thanks.
What caused the cracked manifold ? And where did it crack ?

Bad design and quality I guess...
The crack is where the runners are welded to the plenum.
It's a well known aftermarket intake manifold brand.

Yes, I thought that might be the problem area. Hope schrapnel didn't migrate into the gizzards.
I will let Paddy know as I think he uses a similar manifold. Thanks.

I found the boost leak. You won't believe it.
 
 
 
Chasing a Boost Leak in a Toyota MR2 - YouTube

How bout dat? 
Pretty sure indication that the alloy plate is too thin. Has been flexing till it broke along the weld. The weld being the strongest. Stress concentrator. Thanks for showing us.

Yeah that's my deduction too. I'm getting it strengthened now.

I have bought a new gearbox and am now half way through the process of putting it into the car. 
I'm waiting for some new OEM diff bearings to arrive and then I will get the TRD LSD removed from my old gearbox and put into the new gearbox.
The clutch looks good so I won't be changing that. Everything else on the engine looks good so I won't be messing with any of it. If it aint broke - don't fix it!

I forgot to post this before. This shows the repairs to the intake manifold which had been leaking precious boost!

 
https://www.youtube.com/watch?v=FeBH6XtZW5c
 

The welding may have something to do with the cracking too. Too much heat and not enough on the parent metal can do that too. 

Here's my latest video from SMSP
Prep for Challenge Bathurst 2021 | Toyota MR2 Time Attack - YouTube