When I started, I did everything by hand and it is a pain and takes so much more time. Honestly, it sounds like making your own script would be the perfect choice. You could intergrate it into your current site/pages. php/mysql would be my choice. Course it will take some time getting all the current links into the new databse, but when done, much could be automated.
I made my own link script, sure if I can learn it, you could too..
You could even start with the basic setup and add on over time. Least get it up and running and saving you some time.
Sure you could find some one to do it for you, but I am guessing it would'nt be cheap.
ronnie