The short answer is, yes, the stock Bosch EFI *could* work with the DCNF throttle bodies. BUT it would require the you use the stock sized injectors, the stock fuel pressure, use a sealed airbox with the stock air flow meter attached...... It would basically be a stock EFI setup with a different throttle valve(s). It *may* give you quicker throttle response, but will probably not flow more due to the AFM restrictions.
It is possible to replace the AFM with a MAP type sensor (and additional electronics), but you'd be into it more than MegaSquirt would cost.
Have you gotten a price on these yet? The last time I checked, the TBs/fuelrails/regulator were over $1200.... And that didn't include a manifold! A friend put the DCOE types on his crossflow headed MGB and it ran him $1400. If you were to go down this path, I would suggest motorcycle TBs - VERY cheap on eBay and come with everything except the ECU.