Good question. To be honest, all was working the way I did, it was just the problem with micros() overflowing. But after I learned about Timers, I had this idea of using a timer and not having to worry about things anymore. As there is a problem I have to check, as my project uses a lot of other things that takes time to process. So the PPQ clock could get late and make the midi sequence drift in time, which is bad.
For instance, the SD Card reading and writing takes time to process, and its done a lot, as all the MIDI data is stored in the SD Card.
But anyway, I will do more tests and see what happens now. 
Thanks again for all the great help. I'm sure I will do stupid things in the way, and maybe a year from now I will fix those stupid things... But at least it will work! ;D
Wk