Hmm, interesting. But note a C-input filter will charge instantly to the full peak voltage. You need an L-input filter, typical of a forward converter, at each rectifier. Followed by the polarity switching transistors.
The same should be true of any other load on the transformer. If you need auxiliary supplies, you're probably better off just adding another converter. Bit of a pain, but it won't have 100Hz ripple on it either, and you can control it differently from the main output (e.g., it stays on when the output is disabled / faulted).
I'd suggest a sigma-delta style control, where you either pulse, or skip a pulse, according to whether the output voltage is above or below the ideal value. This won't necessarily reduce the ripple, but most of it will be above the fixed 1kHz in your current approach.
Worth noting that, a pulse should be defined as 1/4 up, 1/2 down, 1/4 up. Not 1/2 up, 1/2 down. That way, the flux doesn't stay to one side, it remains balanced. Also a bit of a pain for the added logic -- though if you've actually got an FPGA handy, it's not a big deal.
Tim