You're graphic is upside down, so I fixed it. You can display graphics better if it is in .png format, something like this...

At this point I'm not sure what I'm looking at. I'll let some other folks take a look.

 

Why are you switching the transistor? I thought this was a PWM-controlled DC power supply. If it is, the transistor will not switch.

 

Here is something I came up quite a while ago for another thread. I've never built it, I don't know if it would work, but it has some of your base concepts.

Where you show a switch on the voltage regulator I have a triangle generator in the form of U1, the 555. This triangle generator is feed into U2B to make a variable PWM signal (sound familiar?). I was thinking of using a LM358 or somesuch, but there is a good chance this design doesn't work, it is a concept drawing only at this point.

MOSFETs are much better than BJT transistors for this application. I suspect you'd need a p channel for your application, and they generally require a switching voltage over 10V (12V works nicely). They are more conductive than BJTs when on, and both are pretty equivalent when off. The key is to avoid that in between state, the linear region. This is true of both BJTs and MOSFETs.