Answer: Congratulations on taking such good care of your plant! Caring for and pruning bonsai plants is such a specialized and intricate form of gardening that it is generally best to see pictures as well as read words when describing something as complex as repotting or pruning. A great resource for you is the American Bonsai Society, c/o Patricia DeGroot, P.O. Box 1136, Puyallup, WA 98371-1136, (206) 841-8992; web site: http://www.absbonsai.org/ They have several publications available to help you begin to decide how to prune your bonsai.
Since you didn't mention which type of juniper you have, it is a bit difficult to make specific recommendations as you will see from the photographs at the site below.
This website provides information about a number of species used for bonsai based on information in Simon Schuster's book, Care of Bonsai: http://www.mnsinc.com/michaelj/bonsai/guide/; there is a page specifically for Japanese Garden Juniper: http://www.mnsinc.com/michaelj/bonsai/guide/garden-juniper.h... and one for Eastern Red Cedar which is another type of juniper: http://www.mnsinc.com/michaelj/bonsai/guide/red-cedar.html.
I hope one of these will apply to yours.
Enjoy your bonsai!
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