Have you read my Moments in Darkness series? Because that covers the time period you are speaking of. It starts a little bit sooner than that, maybe one or two episodes sooner, but it goes through Parting of the Ways and then beyond it with the Tenth Doctor (it's up to just after Girl in the Fireplace and will eventually have more installments) and I think it might be what you are looking for. The first story in the series is Need: http://amberfocus.livejournal.com/36302.html and each story is linked to the next.

I'm glad you enjoy my stories. Thank you.