The core of this is a ME pattern that looks like this: https://i.imgur.com/hMkb5lq.png
That is, the entire sequence of 18 quark catalysts which contains every possible pair, making 2000 bary matter.
This pattern is being requested by the fluid export bus, in crafting mode, on the right side, pointing to an input hatch of the HILE. The interface with the pattern is in the middle, pointed to a HV chest buffer, which points to an input bus of the multiblock. So when AE requests the pattern, all the quarks get sent into this buffer, in the correct order, and then sent to the multiblock at a rate of one second per item (the output speed of the buffer).
The buffer also has a machine controller cover, which is toggled by a ME storage bus, which is in crafting mode and emits a signal while a drop of bary matter is being crafted.
So the whole process looks like this:
- AE requests the pattern to be crafted.
- Quarks get sent to the chest buffer.
- Level emitter turns on.
- Buffer sends quarks to the machine, one at a time.
At some point the correct combination of quarks is hit, and the machine spits out 2000 bary matter back into the system. This completes the ME craft. So the level emitter turns off, and no more quarks are sent to the machine, to save on infinity.