Just got me a new pair of custom made orthotics to treat my shin splints about a month back and have been gradually easing into them. My shin splints have reduced considerably, however discomfort has popped up in other areas (right ankle, on the outer side about an inch from the bottom). Is this normal? Have you experienced niggles cropping up in other areas? How long before I run completely pain free (or is that a dream)?

yes, before and after my runs.

My shin splints have reduced considerably, however discomfort has popped up in other areas (right ankle, on the outer side about an inch from the bottom). Is this normal? Have you experienced niggles cropping up in other areas? How long before I run completely pain free (or is that a dream)?

Minor aches and pains in other areas are expected when you first use orthotics. Before the orthotics, your body compensates for the misalignments by developing some muslces at the expense of others. The orthotics change how you stand and how you run. The muscles that you didn't use before now need to strengthen and I think that's what you're experiencing. As RunB said, don't do long runs in them until your body's accustomed to the changes. The pains should go away soon. If not, talk to your podiatrist.