Hi, I have been researching it for the last year or two. Complete used Hayabusa engines can be brought of Ebay from around $2000 up. Where it gets expensive is the differential/reverse unit which replaces the transmission. These units are also referred to as Forward Neutral Reverse (FNR). If you check the forum www.minibuggy.net there is a lot of useful information about these units here. Some of these diffs/reverse are prone to breaking. There are two units produced that I know of based on the VW transmission case and the feedback on the forum is they do not hold up. The most reliable seems to be the Jeffco & RPM units. Both are chain driven which is not to everyones liking. The Jeffco I sells for just under $3000. The 'RPM' FNR does not have a differential. The price I believe is in the low $2000's. RPM can custom fit a diff at extra cost. There is also a couple of units produced by Quaife. The Quaife Powertec has a diff/reverse and is direct drive (no chain). The price is $4500+, I have not been able to find any user reviews of this unit. There is a unit manufactured in the UK by Elite racing. It has diff/reverse and is direct drive but I have not been able to find any information from users either. In addition to the engine and FNR, you will need a swivel pick-up oil pan which costs around $300, so as to not let the engine run dry of oil when cornering. You would also need to spend money adapting the wiring/ECM, there is information and kits for 1999-2007 engines out there to do this out (2008+ engines there is less info at this time as they are relatively new).
I would still like to go this route and was aiming to keep the car below 1500lbs. With a standard Hayabusa engine 0-60mph would be in the low 4 seconds. Handling should benefit from less rear weight.