OK, firstly:
yes the gearbox (squared above) will come out independently of the engine, IRD has to come off first.
Are you sure its the gearbox and not the IRD cogs, they will clonk and jolt when you boost the power at low speeds
Removing the IRD is a MAMMOTH TASK, give yourself 4-5 hours to remove it, refit it.
There are many awkward parts, such as the coolant hoses going into the IRD. They need to be clamped before dis-connecting, otherwise coolant will go everywhere. This will save you draining the whole system.
IRD/Gearbox will need drained, both driveshafts removed, Prop disconnected, exhaust downpipe removed..............the list goes on.
Some pics of the IRD/gearbox without the 1.8: