Jeez, nice work there! You will not have trouble with this project.
If you already have a spare Mk1 Rabbit diesel engine and gearbox, it will go straight into that Scirocco, since all Sciroccos are Mk1 cars. Dead simple, you won't even have to think. 'Course, that engine will be complete with all rompin stompin 48 horsepower unless you do something to it.
The VW turbodiesel engines have internal differences compared to the earlier non-turbo diesels. For one thing, all the turbodiesels have oil-squirter jets for the bottom of the pistons. Some other internal parts were strengthened but I don't know the details of this. Everyone says that if you want your turbodiesel to live, you should start with a turbodiesel long block, not a regular normally-asthmatic one. It is possible that the later 1.6 normally-asthmatic engines got some (? not sure) of the upgrades on the turbo engines but again, I don't know the details. Someone on
www.vwdiesel.net will know the answer to this for sure, though.
The 1.6 turbodiesels '84(?) - '92 will drop directly in place of the 1.6 regular diesels with the usual minor intake and exhaust fiddling. If the engine came from a Mk2 ('85 - '92 in North America) it will need some engine mount fiddling and possibly accessory-drive fiddling to get it into a Mk1 (i.e. Scirocco), but from what I can gather, all the Mk1 engine mounts and accessory parts will go straight on no problem.
Next up is a 1.9 turbodiesel, engine code AAZ, from Canada, 75 hp in stock form, can be tweaked to 90-ish. These came in Mk3 cars in Canada through to '97 and B4 Passats '93 - '95. They will go into your Rabbit/Scirocco (Mk1) with the usual intake, exhaust, engine mount, and accessory drive fiddling. The bad thing about the AAZ's is that the keyway on the crankshaft that drives the timing belt pulley is weak, and they often get smashed up in 300,000 km give or take, and then the engine goes boom. The 1.6's had the same setup, but with the smaller displacement (and less engine speed fluctuation) it was not a problem. You can substitute a 1Z or AHU (early TDI) crankshaft and timing belt pulley, but if you're going to do that, a different recommendation is below ...
On any of the turbo diesel engines mentioned so far, none of them have intercoolers. You can easily fabricate something so that you have an intercooler and the engine will be much happier for it.
Now, on to the TDI's. If you can get your hands on a 1Z or AHU from a '96 - '97 Passat TDI or a '97 - early '98 Mk3 Jetta, it is the same job to put that into the car as it is to put an AAZ in there, but now you will have to deal with the electronic injector pump. Choice 1, electronic controls - adapt the 1Z/AHU wiring harness and sensors, rig up a throttle pedal position sensor, use the 1Z/AHU ECU, and go all electronic control. Choice 2, fit an injector pump from an earlier turbo diesel and go mechanical.
www.vwdiesel.net - the terminology for this that people have adopted is "m-TDI" for mechanical TDI.
Fitting Mk4 or later engines, or VNT turbochargers, gets way more complicated.
So many choices. How fancy do you want to go?