If you lower the gearbox through the back engine mount you will have an incorrect angle at the rear of the gearbox for the front universal joint, the rear of the gearbox will also be unsupported as the grey engines have the rear mounts at the back of the engine and there is no actual gearbox mount per se.
I have seen the support brace that goes from sill to sill and across the transmission tunnel removed through the transmission tunnel and then an additional braces welded in towards the rear centre floor brace. The floor has then been "stretched" to allow sufficient clearance of the gearbox. Have a look at the various braces in the following link to get an idea of what you need to do. Check out reply no 35 on page 2 and have a look at how Red Devil has fabricated the members and brackets to provide transmission tunnel clearance.
http://fefcholden.org.au/forum/index.php/topic,14706.0.htmlLeaving the original transmission tunnel in is not what I would do, but nevertheless possible. This is far more preferable than trying to lower the rear of the gearbox. To "stretch" the floor is the poor option as this will weaken it.
To be clear, whether you change the tunnel or leave the original tunnel in place you will still need to fabricate subframe members that go from the gearbox subframe member to the subframe member underneath the seat.