The Series 3 engine will fit straight in as they are basicly the same, although the later S3 engines had 5 main bearings in stead of 3, i have a late 3 bearing military block in my s2a. the problem with the clutch master cylender, i take it you do mean the one on the bell housing,i believe that the clutch actuator and master clylender are slightly different.
I have to admit that i have an early s2 gearbox in my 2a, has 1 big advantage over any of the later boxes, you can top the oil up from above. Much nicer than having to get underneath in the winter, shame about the lack of syncro.
Does the top plate from a s2 box fit a s3 box??