To reprogram the computer, do you just drive it for awhile or does someone have to reprogram it?

A software reflash requires someone to update the software with a computer. But it sounds like you have something else going on. Get the valve cover leak fixed and then you may need some hands on testing to see why the engine is running rough. Here is a link if you need to find a shop local to you.https://repairpal.com/repair-shops Alex

First - can you elaborate a bit more on why you think the computer needs to be programmed?