3UZ-FE engine swap into IS300 by Millen - Transmission Adapter Shown
 

Just in case you haven't seen Millens LS430 powered IS300 here is the video that was aired on TV. They sectioned / shortened the front of the Supra manual transmission about an inch. Then they made their own adapter plate that they welded onto the bellhousing which allowed the transmission to basically bolt right up to the engine. I'm pretty sure they used a hydraulic throwout bearing for the clutch because they have lots of money and that's the best way to go. I'm not positive on this but I don't see them going through the hassle of using a manual shift fork and rigging that up to work.

The 3UZ-FE powered IS300 Lexus video if you haven't seen this you should. This car is a sleeper. Navigate or watch the video through until about 7:30 is where they start the work on the transmission.