Orthotics and over correction problems

I have been running fairly long distances for about 30 years. 18 months ago, after finding out that I have got a cartilage problem caused by a leg length difference, I had orthotics made. I asked about the type of running shoes I should use but didn't get any advice so I carried on using Asics Kayanos. I realised that one hip was giving me trouble straight away but the physio gave me exercises and I assumed this was all part of getting used to the orthotics. To cut a long story short, the hip problem got worse and I finally went to a really good running shop last weekend and discovered that the Kayanos were over correcting horribly. I am now in shoes with a much lower heel drop and immediately I can run like normal again. Annoyingly I seem to have weakened my calves and the troubled hip over the last 18 months. Any tips for how I can get things back on track as swiftly as possible without causing other problems? ,I have been told i need to take things quite slowly since the change from the Kayanos is quite significant and my new shoes will be working my calves and hamstrings harder. Thanks