I think your current design will struggle to hit 3A (that poor SOT23 driver transistor), very little chance of it being stable and I don't think your tracking pre-regulator FB loop can be frigged like you think.
I'd split the design into two major parts, develop and prove them seperately:
1. Output stage /w current limit.
2. Tracking switched pre-regulator.
The first part (the output stage), i'd probably look very carefully at what HP have done in the 80's - these supplies were excellent. and the schematics are readily available.
Would probably tackle the switched pre-regulator using a microcontroller (dsPIC33 would be my first choice), as this is really only to reduce the heat generated the absolute performance is not *that* critical. Probably build a control loop at 10KHz with perhaps 100KHz PWM, would be converting absolute current, output voltage, input voltage and requested voltage, probably quite a straightforward algorithm. As Paul Price says, use PWM's to generate the target voltages, these don't need to move quickly.
One problem I've had with PWM generated voltage rails is that they are only as accurate as the processor voltage regulator. I recently got round this using a REF5025 (this was elsewhere in the design) and an ADG749 (being driven by the PWM), super stable.