I've done this conversion in a 32 GTS4. I used an aftermarket ECU (Wolf 3D 4+). The engine itself drops straight in, and bolts up to everything - gearbox, driveshafts, P/S pump, A/C compressor.
The outright majority of Stagea engines are autos - manuals are almost rare as chicken teeth. So you will need a new flywheel, and a new spiggot bearing.
The diffs in a Stagea are 4.08:1 . RB25DET doesn't need 4.375 final drive, so I ended up getting a Stagea rear diff and swapping the crown wheel and pinion over to the R32 diff housing. Also, I don't think the Stageas have any form of LSD rear, so another reason to swap the gears.