There are three distinct generations of R1s out there. This refers to the architecture of the basic engine (motor mounts, all internal components, etc.).

'98-'03 is the first generation (early years had carbs, last 1 or 2 had FI),

'04-'08 was the second generation with different motor mount locations, etc. (went basically unchanged through out the years),

'09 to current is the third generation, again with changes to motor mount locations, etc (these are the cross plane crankshaft engines).