It's not just you...you're missing some utilities.
I had a go at the build, eliminating some modules in the process. I didn't see the point of having huge distortion and stereo delay modules taking up space, so I chucked those and went with a different FX setup. I also got rid of the sequential switch (no sequencer, so...) and modified a few things, and this is what resulted:
I took a BIG cue from your frustration with the current state of capability, and tinkered with this so that it's capable of more elaborate modulation, plus I added a beefier (Pachinko...Marbles clone) random signal module to kick that up considerably.
Top row: This is ALL audio now. "Voice 1" is the Dixie2+/Red Dragon/Javelin set. Then "voice 2" has the stereo oscillators feeding the Squawk Dirty via a Happy Nerding 2x SAM, which provides two stereo inputs to one stereo out, letting you submix the stereo oscillators. Morphagene follows, then I changed the VCAs to a Veils clone (getting back 2 hp for the 2x SAM) and placed that so the VCAs can function as level controls for your mixer strips.
Bottom row: PWRchekr, then a Yarns clone (much more capable than the previous MIDI interface). Pam's is after this, then the Kinks, but after that I added a CVable Logic module, which will allow you to play a couple of timing channels from the Pam's off of each other to create some more complex clocking behavior. Marbles clone is after this, then the Batumi with the Poti expander. And keeping with that, I added a Zadar and its expander; the build now has five EGs, including the one in the Javelin. A Frap 321 provides various CV/mod alteration functions, and I added three more VCAs after that...which will allow your modulation signals some improved capability by adding CV control over modulation amplitudes. Then Maths...and the FX section is now a Happy Nerding FX Aid and a knob.farm Ferry allows two channels of FX send/return for an external FX processor (or two) which can be a much more complex rack device (and those are pretty cheap right now, thanks to VSTs). Lastly, the Befaco output module.
Again, this was done with the "self-modulation" shortcomings in mind; this build now has that dealt with, and the modulation palette is MUCH more complex with the addition of the various bottom row modules and the deletion of the 32 hp's worth of FX modules. That part was a great example of "sexy modules" gone bad, as those took up the space you really needed as modulation modules. Your voices are also now laid out more sensibly, with all audio modules except the FX and output on the top. And yes, there were deletions as I've noted...but this is definitely much more focused on creating complex sounds with considerable internal change, as you'd wanted.