Well taking your existing old server and converting it to an updated ServUO server would probably be a bit of a task especially if you have quite a few custom scripts. Many custom scripts that are 4+ years old are still compatible with ServUO with little to no tweaking, but comparing an outdated RunUO to a ServUO server is the real task. Unless there's a real good reason you want to save your old server I'd say the best approach would be to download a new ServUO and find the custom scripts from your old RunUO server that you want to keep and simply try implementing them.
I recently updated my 1 1/2 yr old ServUO server to the newest ServUO version and that took some time -- I don't even want to imagine what it'd be like going from a highly customized, outdated RunUO server to a new ServUO. I'm not saying it can't be done, but it's up to you whether you have the time/knowledge to take on a project like that.
If most of your old custom stuff is like Daat99OWL custom ore and leather then that can fairly painlessly be implemented on a fresh ServUO install. You may find that ServUO has by default many features that the old RunUO servers didn't and so you might not need alot of your old custom stuff. Basically the difference between ServUO and RunUO currently is that ServUO has a lot more new expansion content than RunUO, such as more Mondain's Legacy and Stygian Abyss quests and content, imbuing support, etc.
Maybe someone else can explain more in depth about the differences --- you could look at the commits to the ServUO repository over the past couple years here:
https://github.com/ServUO/ServUO/commits/master?page=1 but it's pretty monotonous reading and only includes everything that's been done since ServUO went to Git.
tl;dr : probably best to d/l a new ServUO and put whatever old custom scripts you want into that.
