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. I have used QuickScore and Copyist from Sion Software for a few decades, and on my iPad I use an app called Music Studio from Digital Audio Workstation. Other good tools include Sibelius and Finale. I am going to prepare some "How-To" materials on editing HymnSite.com's files using free music notation software from MuseScore. Meanwhile, their online help materials should get you started.