Hi Wolfgang,
I'd recommend you build the MIOS PIC-based board over at
http://www.ucapps.de/. Build the main MBHP Core board, and probably the DOUT board too (although you'll likely only need one chip on the DOUT board if you're only controlling one line).
Once the PIC has been flashed with bootstrap, the core module can be programmed via the MIDI In/Out ports. The main program is configured and setup from a text script which is then 'compiled' and uploaded via the MIOS utility on the website. The file controls the setup of what boards are connected, what inputs/outputs map to what (analog and digital depending on the daughterboards you make and add-on), switches, LEDs, LCDs, joystick, motor faders, MIDI channels, controllers, sysex etc etc
I reckon if you can't do get what you want from it by altering the standard config, then there are plenty of experts on the ucapps forum who will no doubt know exactly how to set it up to do what you want! And I don't think you'll need to write a single line of microcontroller code!
Regards, Paul.
[EDIT: Come to think of it, if you can get your sequencer to transmit MTC (midi time code) on a spare MIDI port then you could set your module up to detect that - it's more reliable than MIDI Clock and Start/Pause/Continue messages]