I'm trying to set up clean bees production, but I'm failing miserably. I kick-start the process and it either just maintains itself and I'm not able to extract clean bees or honey from the process or it just implodes and keeps getting slower and slower... until it can barely sustain itself...

Putting some splitters to force 3/4 of output to be fed back in some places seemed to have improved things, I can at least maintain the process going now, but it still feels useless.
What I have done:
3/4 of Clean larvae goes into apiaries to become Clean Bees.
3/4 of Clean bees goes into Synthetic hives to produce combs.
All combs become honey.
Remaining Clean bees passes in front of Royal jelly apiaries and whatever remais on the belt is fed back into the system.
3/4 of honey goes into queen making apiaries and the other 1/4 into a passive provider that feeds honey to remote resource bees process.

I plan to move the resource making bees to use belts once I get a hang on how to make it actually be able to output more than it seems to need.
EDIT:
(Honey seems to be clogged in front of queen apiaries, so it is outputting more than 1/4 honey, I'll try adding one more queen apiary at a time to see if it scales)

I forgot to mention that everything has Speed Module 3 on all slots.

Ok, I'm dumb, I didn't need to split 3/4 to queens and stuff, I just need to let everything pass in front of the queens apiaries, and if somethings goes through all, I can redirect to other places, ok, the process is consistent queen-wise.

BUT now my Clean bees apiaries are clogged with Clean larvae.

I'm loosing track of the maths lol.
Considering that i have 7 queen apiaries, this will output 70 clean larvae and since I'm redirecting 3/4 to be made into clean bees, without considering crafting times, I'd need 52.5 apiaries to process all at once, I think.
I guess the right thing now would be trying to calculate things considering the crafting times? @_@

Try to use output priority instead of 3/4 splitters

There is a tilable design with perfect ratios here: https://www.factorio.school/view/-LBfVclks5go4FJgpMax
If you get stuck again

It sounds like you are enjoying the mod :)

Thing is, I haven't managed to find the exact number of apiaries to make it so excess larvae go down to queen apiaries.
What I have now consumes all larvae that goes to that section, so if I use an output priority, all larvae will become bees and my queen production will stop.

I tried getting this blueprint that you also sent in another thread in this forum so I could look at it and try to understand, but it fails on import (I'm on 1.0).
It said that it couldn't find some recipes or something like that, I can grab the exact messages the next time I log into the game.

Yes, I'm having great fun trying to make this work.
Solving problems is really fun. XD
Last problem I had was making a kovarex enrichment cycle that didn't hold more than 40 U-235 per centrifuge. It took many tries, but I finally managed.
Might not be perfect in terms of being able to beacon stuff, but I felt accomplished.

Hmm, I made that blueprint back in .16, so I might need to go update it. Thanks for letting me know

If my math is correct, for each queen we can only output 3 clean bees, right?
Because from 10 larvae, we need 1 fed back to make another queen, 2 to make enough royal jelly for the queen, 4 to make the necessary amount of honey for the queen, so from the 10 larvae produced, 7 needs to stay to make another queen.
So if I manage to make something compact, it will only be able to output 3 of the bees each cycle.
If so, I'm starting to realize that I'll need to make a really huge bee production site to be able to support all the other bees. :O
Specially considering the resource queens also need royal jelly and that will take 2 of the 3 outputted bees, and then there would only be one bee to make honey that the resource bees also need.

I'm just not sure about the timings, like, I could do each 3-bee producing alone and kickstart with one queen, but that might make the machines stall waiting for resources... the process would be infinite, but the rate of production might be slow.
Not sure yet on how to approach this.

I'm really enjoying this mod, it's making me think much more than the vanilla game.

You are correct that it only yields 3 bees per cycle, but this is offset by the fact that the bee machines are so small, and that their power drain is fairly low.

I've realized there is a bug that disallows productivity modules in all the machines, so once I fix that the yield should be better

Edit: I was mistaken, there was no bug

I want to make a spotlight video on this mod. Whenever you are satisfied with your beekeeping setup, can you give me your save for this purpose?

Ah, yes, the productivity module really doesn't work! Is that intended? Or simply wasn't coded in?

I haven't got back in the game since my 3 initial posts. lol, I've been grinding it in my head and some paper notes on my free time. XD
I still have some work to finish before I can hop into the game again.
As soon as I'm able to organize the setup and have it running correctly, I can send you my save. :)

The productivity module is working as intended. You cannot use it on the initial clean loop, but it will work for essentially all parts of the ore bee process.

The reason for this is that productivity would make the loop way more positive than I balanced for