I would suggest getting the turbine side lined up and removing the compressor housing before you clock it. If you start rotating it with a gasket that has been on it or 30 ears, you will probably destroy the gasket/o-ring. Best method after rebuilding is to use a new gasket/o-ring that has been lubricated and then you can clock the compressor housing. With the TE06H, there is a C-clip that you have to remove first before you can clock the compressor housing. Being that you are installing a turbo that may be from an earlier car, marking the CRH and the compressor housing may not help at all if you have to clock it to fit it.

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1991 F250 super-cab 7.3 IDI. (rebuilt by me) Banks Sidewinder turbo, hydroboost brakes, new IP and injectors.
2003 S430 - 107K
1983 300SD - Tanoshii - mostly restored ~400K+.
1983 300SD - Good interior. Engine finally tamed ~250K.
Monark Nozzle Install Video - http://tinyurl.com/ptd2tge