Phonogene was my first module ever (Morphagene didn’t exist at the time). It was a great starter, I had other non-modular synths, and my computer…feeding noises from those sources into Phonogene kept me entertained for quite a while.
I just got a Morphagene recently, it’s a really fantastic module. Just about anything will complement it. Wogglebug is a good choice, as you’ll get a clock (which Morphagene loves…being able to start and stop recordings on the beat is great) plus the random modulation will help you skip around between splices.
The system concrete is a really good guide, you can’t go wrong building up a system based on that design. Maths was my second module after Phonogene. Wogglebug probably would have been a better choice, especially for Morphagene. My only change with the system concrete would be to swap the echophon for a erbe verb. I ended up building almost exactly the by-the-book concrete system, except with Clouds and Echophon as my main effects modules for quite a while.