so about 60% of the time in first or second, when the second turbo spools it then lunges the car forward and will not continue to boost (5500 rpm).

But in third, it doesn't have any problems.

Any idea why this would happen?

 

Solenoid problem maybe? Have you checked your soleniod racks to see if anything is broken?? I would check that first and go over all of your vacuum lines. Hope that helps.

 

Gearing has little to do with it, RPM and vacuum/boost pressure does. Lunge=Navy aircraft carrier catapult shot=good.
Check your rubber Y-pipe coupler for cracks that may bleed under high boost. You have a boost guage, right? Do you hear a groaning noise at full boost?