It is no surprise to me--people like the MIDI files at HymnSite.com, but they want to change them "just a little bit." Some people want them to play faster, others want them to play slower. Some want different instruments. Some want introductions. Some want to transpose the music higher, and some want it lower. You wouldn't believe how many different things people want to do. To tell the truth, HymnSite.com's MIDI files were created so that they could be changed. They were originally intended for transposing parts in different keys for wind instruments like trumpet or French Horn. If you want to use them for anything else, you really have to do some customizing.
How do you do this? Well, you will need some kind of MIDI software to do it. I am preparing this "How To" page using Jazz++, a free MIDI sequencing editor that can do just about everything you will need. It is not a "publishing" application, though, so it won't help you print music. I'm keeping my eyes out for a free music publishing application. If you know of one, please let me know at HowTo@HymnSite.com. I usually use MusicWrite for publishing. It is commercial software that does a reasonably good job. You can also consider using commercial products from NoteWorthy, Cakewalk, and Coda Music. Links for each of these can be found in HymnSite.com's HymnStore.