So replacing the Jupiter III with the Mochika XL from Atomosynth was a good idea, it is much more flexible, includes an 8 step sequencer and takes MIDI clock signal.
I have also added a Drum 1.1 from BASTL Instruments with the BASTL MIDI interface. BASTL Instrument is a small Czech company that builds cool little products runningon the Atmega 328 that can be re-programmed/hacked using the Arduino IDE. The DRUM 1.1 comes with cool samples like a lo-fi T909.
Talking about Arduino, this is probably where there is a lot of untapped potential for pedal junkies who want to sync everything together. The solution I have put together so far includes many different products from different companies (Koma Elektronik, Mutable Instruments, Molten Voltage/PedalSync, Empress, etc.), it ended up being expensive and always a bit of a hit and miss affair, some of these products are fragile and not that much pedalboard friendly. I am therefore exploring the Arduino world and have a few things in progress on breadboards. More on this later.
How Did I end up doing it:
I use Mutable Instruments MIDIpal as my main clock. It is accurate and includes a crazy amount of other functions. The master tempo can be defined by simply taping the pot or turning it. The tempo is displayed in BPM on the LCD screen. Simple enough. The ERM Midiclock can do this too so can the PedalSync Master control.
For all the pedals that can receive a MIDI clock signal (Eventide, Strymon, Boomerang, some Moogerfoogers, Pigtronix, etc.) the MIDI clock signal can be routed to them using a MIDI splitter like the Kenton THRU-5, the Midi Solutions MIDI Thru and Quadra Thru, the Pedalsync MIDI Splitty, etc. MIDI was bigger years ago and if you need more than 5 outputs, you can find products that offers more outputs on eBay, look for Forefront Technology FT5, MIDIman Thru 3x8, etc. There is a company in Brazil (EMW) that still manufactures one and it can also be found on eBay.
On the picture below the EHX 8 Step, the Atomosynth Mochika XL, the Koma RH-301, the Eventide Timefactor (far left), the Boss SL-20 and the Rang (both not on the pic) are all taking the Clock Signal with a MIDI cable. It works with Midi cables with 5DIN plugs but with only 3 active pin. Pedals do not need phantom power and I have not found a pedal that requires 5 active pins (yet), this means that you can make your own cables pretty easily.
For all the pedals that have a tap tempo input to plug a remote tap tempo switch, you can use PedalSync CTL-Sync or build it or even something better but based on the chip used. They sell them too.
On the picture below, the Boss PH-3 and the Montreal Assembly Nasa Attribute are both synced to the main tempo via the PedalSync CTL-Sync.
The Warped Vinyl is designed to accept the signal from the Empress MIDIbox. If you have both a Warped Vinyl and the Empress Phaser of the latest Tremolo, it’s a must have. Joel makes/sells the cables if you need one.
On the picture below, both Warped Vinyls are synced this way.
For all the Moogerfoogers and Koma, MIDI to CV converters exist, Kenton, MIDI Solutions do some. But the Koma RH-301 takes care of it superbly well, it can also deal with old synth that can only do DIN sync.
The Goatkeeper is another kettle of fish entirely. To sync it to the main tempo, I use the Roland DB-90 and plug a cable from the headphone output to the Sync input on the Goatkeeper. To sync perfectly it needs a very neat beat, so the DB-90 needs to be in metronome mode and not in drum machine mode otherwise the Goatkeeper will mimic the pattern. It can be actually very cool but it makes things slightly difficult to fine tune with the Goatkeeper’s sequencer as it follows basically 2 different sequences (the pattern from the DB-90 and the pattern set with its own pots).


So now that I have managed to sync everything. I am moving to the next step of this endeavour which is to trigger events based on divisions of the main tempo with limited or no human interactions. Well I'm going to try...
3 things are in progress, and I am awaiting parts from Mouser, Das Musikding and Mammoth:
1. A splitter with a VCA controlled loop (volume) to use the EHX 8Step to create some fuzz/OD riffs in the background.
2. An Arduino based device that allows complete control on the division (subdivisions/multiples) of the main MIDI tempo and can output a signal as MIDI or tap tempo.
3. A circuit that allows the EHX Freeze and the NASA Attribute to capture notes automatically at specific intervals based on a division of the main tempo using the CTL-Sync (for now) – the arpeggiator of the NA being also synced to a subdivision of the main tempo.
This last one should look like that hopefully:

I'm no pedal builder, so many peeps have given me a hand but it looks like it's going to happen. I'll post clips soon.