You can, but there are differences. The main difference between NA and TD VW engines is that the TD engines had piston oil squirters in the block, where the NA engines did not. That being said, many people have run NA blocks in a turbo setup without any ill effects as long as EGT's are kept in check.
I am doing a very similar build, though I rebuilt the engine and had the pistons ceramic coated to help with heat protection. Check the link in my signature for the whole build up.
The NA injection pumps do not have the boost aneroid to increase fueling under boost. You can turn up the fuel in the NA pumps, but they will be smokey until boost builds, it is better to run a TD pump if you are adding turbo to an NA engine.
Finally, a 50-trim turbo might be a bit too large for a 1.6, though depending on how crazy you are going with the build, it might work. I'm running a 45-trim from a Mercedes Diesel, which is a bit bigger than the stock VW T3, many have said it will be too big, but it builds boost just revving it in neutral without any additional fueling, so I have a feeling it will work.
VW used basically the same VE pump for all of the IDI engines, with minor differences through the years. The early 1.5 pumps were as basic as they get, with only a cold-start timing increase lever. The early 1.6's had turbo and non-turbo versions, some had a dual-detent cold start setup, some NA applications had an altitude-compensating aneroid on top, the Eco-Diesel cars had a turbo but an under-fueled NA pump to clean up emissions, etc... The later 1.9 IDI pumps had idle boost when AC was turned on, etc... but essentially they are all very similar pumps.