I may have a resolution to my gearbox rattles. We shall see.
Yesterday I went to visit an auto gearbox specialist for them to have a listen.
They were adamant that the noise sounded like something outside of the gearbox, so inside the bell housing. They said it sounded like the flex plate, or bolts into the torque converter, or something like that is rubbing.
It would explain why the noise seems to be diminishing with time, as whatever is rubbing wears away.
Then on the way home I stopped at a paint shop to get some paint for the outer sills.
On restarting the noise got a loss worse and permanent, so I cut it off. After that it wouldn't start (starter motor not turning over). I left it a few minutes and then it would start, noise gone.
So I'm thinking that I don't have enough clearance from the starter ring and the starter motor teeth, or maybe I have a sticky starter motor that's not retracting enough.
I am using a standard bell housing, torque converter, flex plate, starter ring and starter motor so you would think that this would remain all stock, but, my flex plate is now bolted to a 1.8 K series crank, not a V6. Exact positioning of the the torque flex plate and torque converter compared with the gearbox input/oil pump does depend on the thickness of the converter plate and machining of the bell housing. Maybe (probably) I have it slightly closer that it was as stock and the tolerance of starter motor to starter ring is too close.
The good news is that if true it's easy to fix. It's just removing and repairing or replacing the starter motor. Probably it could do with a spacer to bring it back a bit. If the starter motor is ruined they aren't expensive. At least I won't have to drop the IRS and gearbox again. So I'm hopeful.