Hey Greg
I've never ridden a 1st gen, but normally I would have pointed you towards the rear shock, not enough rebound damping, or too soft a spring, or both. But, IIRC you've already got a 3rd party shock on board. Have you got the forks dropped?
All the 2nd gen's I've ridden are rock solid at speed. The only issue I've ever had is a slight bit of headshake decelerating between 75-65 km/hr (45-35 mph). This was on my 2G 600, with 120/60 Bridgestone fronts WITH a centre groove.
Moving to a 120/70 front (like the 1200) with no centre groove (Michelin Pilot Road and Bridgestone BT-021) cured the issue, even with a longer B12 shock and dropped forks.