So, after i finished my thesis, i got to work putting together my diesel engine with the parts i had bought earlier.
I carefully cleaned the bottom end of the engine, removing the old bearing journals and replacing with new, standard sized ones. I checked the clearances with some plastigauge, and it measured well. The new crankshaft from a 1.6l petrol engine (the bottom crankshaft in the photo below- remarkably exactly the same as the diesel one.) slotted in nicely, with plenty of oil splashed around for good measure, and strict adherance (within environmental limts) to the "cleanliness is next to godliness" rule.
The oil pump (checked and cleaned), slotted in nicely, and the flywheel and sump went back on.

The engine was timed, the timing belt installed and tensioned, and everything checked over thoroughly, ready for the installation.

This is a photo of the engine bay with the petrol engine installed.
The fuel lines required changing to larger ones (in order to allow good flow of the more viscous diesel fuel). This required the soldering in of a larger pickup line in the fuel tank, and changing the fuel lines to diesel spec ones (8mm).


And then, 8 hours of this (show below)


And she was a diesel!
Note the larger starting battery
And a new sticker on the top of the window!

This is a pic of my diesel golf on a rally with some other guys from the forum. My car was 5 years older than any of the cars present, and 20 years senior of most! This was the first real long run. It was a hard run (up the blue mountains and back via the bells line), but the engine still managed to do an excellent 5.3l/100km (including fuel leaks). Better than the souped up Mk4 GTIs which were doing only 400km on a 50l tank (15l/100?)