Well, I like the conversion idea, but I feel that it hasn't been fully thought out/discussed.
My thoughts;
You want to fit a tddi engine to a MK5 = good, I'd like to see one done.
The suggestion to convert it to a manual pump = doesn't make any sense, as this is the bit that makes all the noise
(the reason for your conversion in the first place)
I've personally known of both quiet and noisy Bosch mechanical pumps. So I would have though it would have been a case of finding a quiet/er pump for your di
If it was me and wanted to go ahead with this conversion, I'd be looking for a complete running van (tddi), with a quiet running engine/pump and transfer the whole lot
Yes, the gearstick may interfere with the handbrake, so you'll have to decide to crank it and or "adjust" the handbrake, or have an adapter plate made to accommodate the MK5 box.
Whatever you decide, good luck with the conversion and I look forward to whatever you decide and how it works out