I've seen source resistors used many times for MOS overcurrent protection. I did think about doing the same for loop control. So...If I understand your idea:
1) Switch is on 2) Switch off at peak switch current or peak of integrator 3) Stall until integrator valley point reached 4) Go to 1It'll probably work. I'll think about it. Do you know if source resistors increase EMI? When the switch turns on the Cuk network gets lifted fast by the Vdrop on the source resistor.
Aside from that....Maybe I could monitor both the mos and catch diode currents....I'll look into that after I get some sleep..
Thanks for the thought.
D from BC