In all honesty there is far too much to go into here, but there are a few basic steps to ensure reliability first.
The engines main downfall apart from the bore/stroke combination were the clutch and the pinch bolts in the gudgeon pins.
These engines can however be made to go quite well. If you intend using it, the first thing to find out is which clutch and primary gear is fitted. If it has the wet primary gear with the oil seal in the flywheel then it is best to change the primary gear to a later one and plug up the oil hole in the crank tail. From there you can start to make the engine reliable without changing how it looks when reassembled.
More details can be found on the MK1 Performance home page about how to do this. Then you will need to do some research before rebuilding the engine. They are mainly the same as any other A series with just a few quirks. I have a 997 and have used the original engine before retiring it for a similar replacement.