Just the person I wanted to answer this question.....

Yes I forgot about that. PK is written into all NON Clustered index. Another point that makes chosing the right column as a PK.

So changing from NON CLUST to CLUST will not affect Query Optimiser and my current NON Clustered indexes should be used in the same way.

Are you saying that although my Clustered index was created successfully my Non Clustered indexes were still rebuilding in the back ground causing blocks.

Carrying on changing my NON CLUSTERED PK to CLUSTERED PKs should not have any real negative effects on the system if it is done when there is enough time for all the indexes to rebuild before a request is made for the resource.