What did you use to decompile them into a project that was actually good enough to read through, change the needed things and compile it again?
I just used Reflector, which, at the time was free. There were a few issues that I had to tweak since reflector didn't do well with things like switch statements ... but for the most part it wasn't too bad. I was able to discern most of the munged variable names just by looking at the code and being familiar with the domain of the company.
That reminded me of a company I worked at. We were moving to a new datacenter, and the job of auditing and moving all of the scheduled tasks fell to me. A good 75% of the scheduled tasks were .exes for which we did not have the source code; and they all had connection strings hardcoded.
Thankfully, they were built in .NET, so I was able to decompile them, move the hardcoded stuff to .config files, and get it moved. But boy did that make me mad at the institutionalized laziness and sloppiness.