Call me stupid.....
I don't always do requests. But, I'll make an exception in this case.
You're stupid.
Bear in mind, I'm not really qualified to make the evaluation.

but it still would only just start on full choke and die without the choke being on full. To cut a long story short, and after hours of messing about with mixture screws, new spark plugs/leads and even new air filters, it still will only run on full choke
I'm guessing you didn't pull out the pressed in slow jets, cleaning them and the passageways behind them during your cleaning. This will leave you with very little fuel for low throttle positions. And, the choke will bump up the throttle and increase vacuum to draw bonus fuel from the main throttle valve to get it running at all.
there are 2 pipes which look the same as the inlet pipe for the fuel (slightly smaller and are made of black plastic, not metal, situated in between the carbs. What do they do?
Could these be float bowl vents? Your original carbs should have bowl vents, too. And, interlinking tubes for this purpose, also.
I have no hard data for support. But, could these PD51A carbs be from a CB500 K3? We didn't get those in the states. But, it seems odd that the original air box couplers wouldn't work. I dunno.
Don't call me stupid.

Cheers,