I finally got my old money pit back on the road (1994 SW20 - now with a Celica GT4 3S-GTE engine swap of unknown origin or vintage - I am sure I'll be back with plenty more issues), and I am not used to the exhaust drone any more (been years off the road).
 
The little cabin vent behind the driver right shoulder looks to be where the peak of the noise is coming in (my 3" exhaust exist on that same right hand side). Is it possible to dampen that little vent or block it up without suffocating? I'm assuming there's a ton of air leakage elsewhere anyway. I couldn't see a way to remove it from the outside, and on the inside it's just some holes in the internal b-pillage moulding, not a piece to remove.

Are you sure the sound is coming from that vent? In the small MR2 cabin sometimes it can be hard to tell. 
I've been told it is tricky removing it and it's easy to break the clips when trying to get it off.
Maybe try tape over the outside just to block it to see if it makes any difference before you bother.

Yeah I guess I'm just assuming. I'll pop a temporary makeshift muffle patch over it and see how I go.

There may be a hole in the firewall I.e. A missing rubber bung.

Is that something I can find myself, or does the engine need to come out ? (Please god no)

Get a length of garden hose, stick one end in your ear, the poke the other end around inside the cabin behind the seat while the engine is running. If there is a leak, you will be able to hear where it is through the hose.

You have a hidden camera set up near my car to record the hilarious nature of this test, don't you? But cheers for the tip

You could make the garden hose more sensitive if you tape a small plastic funnel to the end of it.
Great for tracking down other noises as well.
Or even better, ask your doctor to lend you a stethoscope. 

Done the funnel in the hose trick, works brilliantly for finding hissing leaks around an engine and no reason why
it won't work in this case. Quite precise.
I am in the middle of soundproofing my Sdub and behind the panel behind the driver's shoulder, is a hole for the seat belt mounting and a hole for the rear crap speaker (removed). That cavity brings a ton of fan and rear tyre noise into the cabin. The same cavity on the other side also, but no fan. If there is one place to fix, that is it. I have lined the cavity with stick on vinyl and filled the cavity (mind a couple of cables) with high density foam. All up 2hrs and $40 (at a guess.) I need to complete some other tasks before driving to confirm the result. 

Did it work?