Depending on the code scanner you are using, the scanner may or may not run the onboard tests. The cheaper code scanners just read the trouble codes stored on the computer. The more complex/expensive scanners will read codes and actually run the onboard diagnostic tests as well.
I'm glad you found someone willing to work with you on the muffler. It always helps to have friends "in the business." I wouldn't be surprised if you found more than a rusted out muffler. You might have exhaust lines rusted out, a rusted catalytic, or more.
As far as the code reader goes, we are using a cheap one, my dad got it for around $90. However, the neighbor who manages the muffler shop has a big expensive code reader that he is going to scan the codes with sometime this week. (Hopefully) He actually told us that a catalytic converter could be ruined and I really hope it's not because he said it could be an expensive fix. We do have quite a few leaks in various systems but they are relatively minor and shouldn't be affecting things too much at the moment.
I know that you did not ask about this here but I figured I would point it out anyways. I am not the only one working on the van...I have zero experience around cars other than the little bits of things I have picked up from this van and from this website. My step-dad used to do car audio installation and he used to work in a garage. He knows alot about cars and has done all of the mechanic work on the van so far. So I am not alone in this quest to repair this van.
I will definitely keep you guys up to date with everything that I do with the van. As I said in the main post though, money is tight at this time and that is mostly why we have not done a lot of work on it. Hopefully when Christmas comes around I will get some money from the outer ring of family and put it into the van.
For now though, Happy Vannin' Everyone.