G'day Steve,
My thoughts would be mount the gearbox and shafts into the vehicle in their natural position and taking a few measurements of the remaining space between the gearbox and drivers side chassis rail to get an idea how close the 2GR will sit to the chassis rail and the furniture that lives around there like ABS, power steering etc.
This should give a reasonable indication how much extra space you will have to sandwich an adaptor plate between the E box and the 2GR, as an adaptor plate (no doubt a custom made one in this instance) will add around 10-12mm to the overall width of the engine/gearbox combo which could make all the difference in the clearances.
The idea would be to try and keep the GT4 box in as close as original position as possible otherwise, as you mentioned, it will introduce all sorts of headaches with tailshaft angles and modifying driveshafts, let alone the headaches of re-mounting the box.
Terry's readings on the Road & Track website suggest that only the passenger side short shaft can be shortened on the E-series boxes, otherwise a custom/hybrid shaft/s will be required, unless something from the Toyota catalogue may just work, thinks V6 Camry shafts, MR2 shafts etc etc.
As far as cutting and shutting the 2 bellhousings are involved, it would have to be some heavy duty welding as, like you say, the gearbox supports the engine weight as well as the box.
Good luck with it!
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