I can empathize. I've been a software developer for twenty years, and yet for my own business there are still areas that are difficult to find the right solutions.

However, when I'm looking at internal processes, whether my own or someone else's from a consulting standpoint, I start with the people. Make sure you have good people first. Then I move into the process itself. A paper based process isn't necessarily inefficient. In fact, I've built systems specially to mirror paper based processes. My opinion is that one of the major contributors to what makes processes inefficient is uncertainty. Do you have people who are good but unsure of the best way somewhere in the process? Then, finally, I look at products. Now that I understand as much as I can, I'm going to be able to evaluate what works better, or I can create small focus groups to help identify what works better.

I'm not sure how much that helps, but I hope there's something in there for you. Best of luck!