Gen-2 and Gen-3 Transmissions are completely interchangeable, save the Speedo Sensor not in a Gen-3 that would have to be added. HOWEVER, a Gen-2 trans is WEAKER than a Gen-3 trans internally. Gen-2's use a 2-peice countershaft with a 5/6/R weakness, where Gen-3's use a 1-peice countershaft without the issue.
That said, go with a Gen-3 Trans.
It is certainly worth looking into a gen-4 (2008) trans, though this will require a little screwing around and a new Driveshaft. I am also not 100% positive about the spline compatibility of the input shaft, you may need to change to the 2008 Clutch and Flywheel as well.
PS- 2300.00 is a little high for a Used Gen-3 IMHO, considering you can get a 2008 trans from the same guy for 700 more, or G-Force variation for a little more than that. The T-56 is not a rare nor super-expensive trans by any means.