I have been driving my R1 powered roadster for just on a year.. what a blast! The R1 (2006 model) was very fast and sounded great, but for a couple of reasons, I have decided to replace the bike engine with a Toyota Gen 4 3sgte motor and a 6 speed altezza J160 gearbox.
Firstly, as I do a mix of track days and highway cruising, I didn't think the Yamaha was going to last very long, and to find a replacement engine here in NZ is almost impossible. Secondly, 6500 rpm at 60mph gets very annoying after an hour or so of cruising.
The gen 4 motor is found in a 4wd layout in the GT-T Caldina wagon. It has a C15 turbo and is rated stock at 260hp. The Altezza J160 box bolts straight up to the 3sgte motor, and gives a nice spread of ratios with a 4.1 rear drive. I am using the stock ecu... I don't think I am going to need any extra boost or power.
You can follow the build diary at:
http://www.lotus7.co.nz/forum/viewtopic.php?f=16&t=1509
http://www.lotus7.co.nz/forum/download/file.php?id=709