First, you already have the best block out there. No need for anything else. Second, I would keep the crank, but buy a set of good I beam rods and light weight pistons with a set of Total seal rings. Also, use a standard oil control ring. The B heads are good, you could send them to Total Engine Airflow, for a port/polish/valve grind. I would also consider upping the compression to 10/10.25 to 1. You can keep the stock intake, but have it ported and polished. If you decide on using the 96-98 Cobra intake, you will need to find a set of C heads.
Since you have so many miles on the car, I would recommend a trans rebuild/driveshaft replacement/rear centersection rebuild. Of course, the best thing for the MKVIII would be a set of 3.55 or 3.73 gears for a little more pull. OH, and don't forget to really clean the IMRC plates, while you have the engine apart.
Edit: Almost forgot, good time to upgrade the water pump to either a cobra or aviator pump.